Last updated: 2021-07-29

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Previous step

Get BLUPs combining all trial data: Combine data from all trait-trials to get BLUPs for downstream genomic prediction. Fit mixed-model to multi-trial dataset and extract BLUPs, de-regressed BLUPs and weights. Include two rounds of outlier removal.

Read pedigree

Read the pedigree I downloaded for IITA

library(tidyverse); library(magrittr)

ped<-read_delim(here::here("data/DatabaseDownload_2021May04","pedigree.txt"), 
           delim = "\t")

Number of full-sib families?

ped %>% distinct(Female_Parent,Male_Parent) %>% nrow()

[1] 1672

Filter: Keep only complete pedigree records.

ped %<>% 
  filter(!is.na(Female_Parent),
         !is.na(Male_Parent))

Summarize distribution of full-sib family sizes

ped %>%   
  count(Female_Parent,Male_Parent) %>% arrange(desc(n))  %>%  summary(.$n)

 Female_Parent      Male_Parent              n          
 Length:1451        Length:1451        Min.   :  1.000  
 Class :character   Class :character   1st Qu.:  1.000  
 Mode  :character   Mode  :character   Median :  3.000  
                                       Mean   :  5.909  
                                       3rd Qu.:  7.000  
                                       Max.   :275.000

ped %>% head

# A tibble: 6 × 4
  Accession       Female_Parent      Male_Parent        Cross_Type
  <chr>           <chr>              <chr>              <chr>     
1 TMS13F1002P0001 IITA-TMS-IBA930265 IITA-TMS-MOK980068 biparental
2 TMS13F1002P0002 IITA-TMS-IBA930265 IITA-TMS-MOK980068 biparental
3 TMS13F1002P0003 IITA-TMS-IBA930265 IITA-TMS-MOK980068 biparental
4 TMS13F1002P0004 IITA-TMS-IBA930265 IITA-TMS-MOK980068 biparental
5 TMS13F1002P0005 IITA-TMS-IBA930265 IITA-TMS-MOK980068 biparental
6 TMS13F1002P0006 IITA-TMS-IBA930265 IITA-TMS-MOK980068 biparental

Match SNP-to-pedigree names

Goal is to identify DNA samples names for listed accessions and parents in the pedigree. Important to choose same samples used in genomic predictions where possible, esp. phenotyped training clones.

However, there may be non-phenotyped clones that are genotyped genomic selection progeny, which I still want in my analysis.

First with the union of the parent and accession IDs in the pedigree.

pednames<-union(ped$Accession,union(ped$Female_Parent,ped$Male_Parent)) %>% 
  tibble(germplasmName=.)
pednames$germplasmName %>% length # number of names in ped

[1] 8276

Add a “Cohort” variable corresponding to the genetic groups or cycles in the germplasm.

pednames %<>%
  mutate(Cohort=NA,
         Cohort=ifelse(grepl("TMS18",germplasmName,ignore.case = T),"TMS18",
                       ifelse(grepl("TMS15",germplasmName,ignore.case = T),"TMS15",
                              ifelse(grepl("TMS14",germplasmName,ignore.case = T),"TMS14",
                                     ifelse(grepl("TMS13|2013_",germplasmName,ignore.case = T),"TMS13","GGetc")))))
pednames %>% 
  count(Cohort)

# A tibble: 5 × 2
  Cohort     n
  <chr>  <int>
1 GGetc    343
2 TMS13   2627
3 TMS14   1979
4 TMS15   1236
5 TMS18   2091

The names in the pedigree downloaded from cassavabase should match the names in the germplasmName variable in the plot-basis pheno data, also downloaded from cassavabase.

From that plot-basis data, make a data.frame of the unique germplasmName-to-FullSampleName matches, where FullSampleName is the column with names matching VCF files / DNA samples.

dbdata<-readRDS(here::here("output","IITA_ExptDesignsDetected_2021May10.rds"))
phenos2genos<-dbdata %>% 
  distinct(GID,germplasmName,FullSampleName) %>% 
  filter(!is.na(FullSampleName))
phenos2genos %>% head

# A tibble: 6 × 3
  germplasmName       FullSampleName     GID               
  <chr>               <chr>              <chr>             
1 IITA-TMS-IBA30572   I30572:250253643   I30572:250253643  
2 IITA-TMS-IBA8200058 I8200058:250304538 I8200058:250304538
3 IITA-TMS-IBA9102324 I9102324:250090766 I9102324:250090766
4 TMEB117             TMEB117:250253666  TMEB117:250253666 
5 TMEB1               TMEB1:250253593    TMEB1:250253593   
6 IITA-TMS-IBA920326  I920326:250090768  I920326:250090768

How many from each cohort in the pednames match a germplasmName with a FullSampleName in the plot-basis trial data?

pednames %>%
  inner_join(phenos2genos) %>% 
  count(Cohort)

# A tibble: 5 × 2
  Cohort     n
  <chr>  <int>
1 GGetc    162
2 TMS13   2422
3 TMS14   1517
4 TMS15    858
5 TMS18    982

So about half of all the germplasmName in the pedigree I downloaded are genotyped and match plot-basis data that I have.

Just to check: does that mostly correspond to the number that have a BLUP for at least one trait?

blups<-readRDS(file=here::here("output","IITA_blupsForModelTraining_twostage_asreml_2021May10.rds"))
blups %>% 
  select(Trait,blups) %>% 
  unnest(blups) %>% 
  distinct(GID) %$% GID -> gidWithBLUPs
pednames %>%
  inner_join(phenos2genos) %>% 
  filter(FullSampleName %in% gidWithBLUPs) %>% 
  count(Cohort)

# A tibble: 5 × 2
  Cohort     n
  <chr>  <int>
1 GGetc    162
2 TMS13   2402
3 TMS14   1517
4 TMS15    837
5 TMS18    981

Almost all of those also translate into a BLUP for at least one trait.

But I want haplotypes of genotyped progeny in the pedigree even if they aren’t phenotyped.

The *.fam file for the RefPanelAndGSprogeny VCF I will ultimately use to extract haplotypes and do predictions with is already in the data/ directory because it’s used in the standard match-genos-to-phenos step.

gids_in_fam<-read.table(here::here("data",
                                   "chr1_RefPanelAndGSprogeny_ReadyForGP_72719.fam"), 
                        stringsAsFactors = F, header = F)$V2
length(gids_in_fam)

[1] 21856

Split the names based on a “:” for the GBS samples, and “_A” seems to work (for IITA) to split the DArT sample ID from the germplasmName for DArTseqLD samples. The suffix / ID added to DNA sample names at DARt seems to vary depending on what gets submitted to them. GBS-era samples (almost) 100% had the “:” separator.

gids_in_fam %<>% 
  tibble(FullSampleName=.) %>% 
  separate(FullSampleName,c("germplasmName","DNA_ID"),":|_A",remove = F)
gids_in_fam %>% 
  filter(grepl("TMS18",FullSampleName)) %>% nrow()

[1] 2420

There are 2420 “TMS18” clones genotyped.

981 of them are in the pedigree and phenotyped.

How many of the pednames without genos+phenos have genos-only?

pednames %>%
  anti_join(phenos2genos) %>% 
  inner_join(gids_in_fam) %>% nrow()

[1] 39

Only 39 new pedigree lines get matched to genos…. none from TMS18.

Why are there so many genotyped “TMS18” that don’t have pedigree?

I would expect more lines to exist and have a pedigree than we ultimately genotype.

But anything genotyped should be pedigreed.

I cannot solve this problem and will move on without those lines.

pednames2genos<-pednames %>%
  inner_join(phenos2genos) %>% 
  bind_rows(pednames %>%
              anti_join(phenos2genos) %>% 
              inner_join(gids_in_fam %>% select(-DNA_ID)))
pednames2genos %>% count(Cohort)

# A tibble: 5 × 2
  Cohort     n
  <chr>  <int>
1 GGetc    162
2 TMS13   2424
3 TMS14   1519
4 TMS15    893
5 TMS18    982

Now make a pedigree with both Accession and parent names matching the genos (FullSampleName) rather than phenos (germplasmName).

ped2genos<-ped %>% 
  rename(germplasmName=Accession) %>% 
  select(-Cross_Type) %>% 
  inner_join(pednames2genos %>% select(-GID)) %>% 
  left_join(pednames2genos %>% 
              select(-GID,-Cohort) %>% 
              rename(Female_Parent=germplasmName,
                     DamID=FullSampleName)) %>%
  left_join(pednames2genos %>% 
              select(-GID,-Cohort) %>% 
              rename(Male_Parent=germplasmName,
                     SireID=FullSampleName)) 
ped2genos %<>% 
  filter(!is.na(FullSampleName),
         !is.na(DamID),
         !is.na(SireID))

In the end, considering only pedigree entries where the entire trio (offspring + both parents) are genotyped, the pedigree has 5921 entries to check.

ped2genos %>% count(Cohort,DamID,SireID) %>% 
  ggplot(.,aes(x=Cohort,y=n,fill=Cohort)) + 
  geom_boxplot(notch = T) + theme_bw() +
  ggtitle("Distribution of family sizes (genotyped only)")

Version	Author	Date
e66bdad	wolfemd	2021-06-10

ped2genos %>% 
  count(Cohort,DamID,SireID) %$% summary(n)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   3.000   6.023   8.000  95.000

Number of families with at least 10 genotyped members, by cohort:

ped2genos %>% 
  count(Cohort,DamID,SireID) %>% 
  filter(n>=10) %>% 
  count(Cohort)

# A tibble: 5 × 2
  Cohort     n
  <chr>  <int>
1 GGetc      1
2 TMS13    101
3 TMS14     58
4 TMS15     17
5 TMS18     16

ped2genos %>% 
  select(FullSampleName,DamID,SireID) %>% 
  write.table(.,file=here::here("output","ped2genos.txt"),row.names=F, col.names=F, quote=F)

## Potential sires and dams files
ped2genos %>% 
  select(FullSampleName,DamID) %>% 
  write.table(.,file=here::here("output","potential_dams.txt"),row.names=F, col.names=F, quote=F)
ped2genos %>% 
  select(FullSampleName,SireID) %>% 
  write.table(.,file=here::here("output","potential_sires.txt"),row.names=F, col.names=F, quote=F)

Prep. Genomic Data

Move to remote server, with Python 3, to use AlphaAssign.

AlphaAssign Documentation

Static downloaded version of AlphaAssing in code/AlphaAssign-Python/.

AlphaAssign will accept a binary plink fileset.

I have one for the “RefPanelAndGSprogeny” VCF set, here: /home/jj332_cas/CassavaGenotypeData/nextgenImputation2019/ImputationStageIII_72619/

Same filenames as the VCFs chr*_RefPanelAndGSprogeny_ReadyForGP_72719..

Concatenate across chromosomes.

Concat chroms

require(furrr); options(mc.cores=18); plan(multiprocess)

pathIn<-"/home/jj332_cas/CassavaGenotypeData/nextgenImputation2019/ImputationStageIII_72619/"
pathOut<-"/home/jj332_cas/marnin/implementGMSinCassava/data/"
nameOfchromWiseVCFs<-"RefPanelAndGSprogeny_ReadyForGP_72719"
chroms<-1:18
furrr::future_map(chroms,function(chroms){ 
  system(paste0("tabix -f -p vcf ",pathIn,"chr",chroms,"_",
                nameOfchromWiseVCFs,".vcf.gz")) })

system(paste0("bcftools concat --allow-overlaps ",
              "--output ",pathOut,
              "AllChrom_",nameOfchromWiseVCFs,".vcf.gz ",
              "--output-type z --threads 6 ",
              paste0(pathIn,"chr",chroms,"_",nameOfchromWiseVCFs,".vcf.gz",
                     collapse = " ")))

Convert to binary blink (bed/bim/fam)

pathIn<-"/home/jj332_cas/marnin/implementGMSinCassava/data/"
pathOut<-pathIn
vcfName<-"AllChrom_RefPanelAndGSprogeny_ReadyForGP_72719"
system(paste0("export PATH=/programs/plink-1.9-x86_64-beta3.30:$PATH;",
              "plink --vcf ",pathIn,vcfName,".vcf.gz ",
              "--make-bed --const-fid --keep-allele-order ",
              "--out ",pathOut,vcfName))

Run AlphaAssign [attempted but not used]

First try to run AlphaAssign

cd /home/jj332_cas/marnin/implementGMSinCassava/code/AlphaAssign-Python/

python AlphaAssign.py bfile=/home/jj332_cas/marnin/implementGMSinCassava/data/AllChrom_RefPanelAndGSprogeny_ReadyForGP_72719 \
out=/home/jj332_cas/marnin/implementGMSinCassava/output/alphaAssignOutput_iita_pedigree.txt \
pedigree=/home/jj332_cas/marnin/implementGMSinCassava/output/ped2genos.txt \
potentialSires=/home/jj332_cas/marnin/implementGMSinCassava/output/potential_sires.txt \
potentialDams=/home/jj332_cas/marnin/implementGMSinCassava/output/potential_dams.txt \
checkPedigree=TRUE fullOutput=TRUE

Results did not seem right. Most parents rejected.

Try again, after reviewing emails with Andrew Whalen from 2018, try running without the pedigree supplied.

cd /home/jj332_cas/marnin/implementGMSinCassava/code/AlphaAssign-Python/

python AlphaAssign.py bfile=/home/jj332_cas/marnin/implementGMSinCassava/data/AllChrom_RefPanelAndGSprogeny_ReadyForGP_72719 \
out=/home/jj332_cas/marnin/implementGMSinCassava/output/alphaAssignOutput_iita_pedigree \
potentialSires=/home/jj332_cas/marnin/implementGMSinCassava/output/potential_sires.txt \
potentialDams=/home/jj332_cas/marnin/implementGMSinCassava/output/potential_dams.txt \
checkPedigree=TRUE fullOutput=TRUE

The call above threw an error at the very end of a 6 hour run, and left no output or record of the log.

**ABORTED use of AlphaAssign for current purposes. Return to an approach I originally worked out in 2016 using the IBD calculator in plink1.9.

Run plink IBD (–genome)

Alternative to the below: Could compute everything manually based on mendelian rules. Kinship coefficients directly from the relationship matrix used for prediction would also be useful, for example, the estimated inbreeding coefficient of an individual is 1/2 the relationship of its parents.

PLINK1.9 pipeline to use:

Subset whole-pop. plink file (AllChrom_RefPanelAndGSprogeny_ReadyForGP_72719) to only lines in the pedigree.
LD-prune --indep-pairwise 100 25 0.25 stringent, but somewhat arbitrary
Compute IBD-relationships --genome
Parent-offspring relationships determination (see below)

Determine parent-offspring relationship status based on plink IBD:

should have a kinship \(\hat{\pi} \approx 0.5\).
Three standard IBD probabilities are defined for each pair; the probability of sharing zero (Z0), one (Z1) or two (Z2) alleles at a randomly chosen locus IBD.
The expectation for siblings in terms of these probabilities is Z0=0.25, Z1=0.5 and Z2=0.25.
The expectation for parent-offspring pairs is Z0=0, Z1=1 and Z2=0.
Based on work I did in 2016 (never published), declare a parent-offspring pair where: Z0<0.313 and Z1>0.668.

ped2check<-read.table(file=here::here("output","ped2genos.txt"),
                      header = F, stringsAsFactors = F)

pednames<-union(ped2check$V1,union(ped2check$V2,ped2check$V3)) %>% 
  tibble(FID=0,IID=.)
write.table(pednames,file=here::here("output","pednames2keep.txt"), 
            row.names = F, col.names = F, quote = F)

Checked plink’s order-of-operations and combing –keep and –indep-pairwise in the same filter call should result in the correct ordering of subset samples first and then LD prune.

cd /home/jj332_cas/marnin/implementGMSinCassava/
export PATH=/programs/plink-1.9-x86_64-beta3.30:$PATH;
plink --bfile data/AllChrom_RefPanelAndGSprogeny_ReadyForGP_72719 \
  --keep output/pednames2keep.txt \
  --indep-pairwise 100 25 0.25 \
  --genome \
  --out output/pednames_Prune100_25_pt25;

Creates a 2GB *.genome, 5634 samples worth of pairwise relationships.

cd /home/jj332_cas/marnin/implementGMSinCassava/
export PATH=/programs/plink-1.9-x86_64-beta3.30:$PATH;
plink --bfile data/AllChrom_RefPanelAndGSprogeny_ReadyForGP_72719 \
  --indep-pairwise 100 25 0.25 --out output/Prune100_25_pt25;
plink --bfile data/AllChrom_RefPanelAndGSprogeny_ReadyForGP_72719 \
  --extract output/Prune100_25_pt25.prune.in --genome \
  --out output/AllChrom_RefPanelAndGSprogeny_ReadyForGP_72719_Prune100_25_pt25

That wastefully creates a 40GB *.genome file with all pairwise relationships.

Brute force solution is to read that, grab the needed relationships, and delete it….

library(tidyverse); library(magrittr); library(data.table)

genome<-fread(here::here("output/", 
                         "pednames_Prune100_25_pt25.genome"),
              stringsAsFactors = F,header = T) %>% 
  as_tibble

ped2check<-read.table(file=here::here("output","ped2genos.txt"),
                      header = F, stringsAsFactors = F)

head(genome)
# # A tibble: 6 x 14
#    FID1 IID1      FID2 IID2    RT       EZ    Z0    Z1     Z2 PI_HAT   PHE   DST
#   <int> <chr>    <int> <chr>   <chr> <int> <dbl> <dbl>  <dbl>  <dbl> <int> <dbl>
# 1     0 TMS15F1…     0 TMS15F… OT        0 1     0     0      0         -1 0.727
# 2     0 TMS15F1…     0 TMS15F… OT        0 0.892 0.056 0.0525 0.0805    -1 0.765
# 3     0 TMS15F1…     0 TMS15F… OT        0 1     0     0      0         -1 0.723
# 4     0 TMS15F1…     0 TMS15F… OT        0 1     0     0      0         -1 0.729
# 5     0 TMS15F1…     0 TMS15F… OT        0 0.407 0.593 0      0.296     -1 0.780
# 6     0 TMS15F1…     0 TMS15F… OT        0 1     0     0      0         -1 0.721
dim(genome)
# [1] 15868161       14

ped2check_genome<-genome %>% 
  semi_join(ped2check %>% rename(IID1=V1,IID2=V2)) %>% 
  bind_rows(genome %>% semi_join(ped2check %>% rename(IID1=V2,IID2=V1))) %>% 
  bind_rows(genome %>% semi_join(ped2check %>% rename(IID1=V1,IID2=V3))) %>% 
  bind_rows(genome %>% semi_join(ped2check %>% rename(IID1=V3,IID2=V1)))
saveRDS(ped2check_genome,file=here::here("output","ped2check_genome.rds"))

cd /home/jj332_cas/marnin/implementGMSinCassava/output/;
rm pednames_Prune100_25_pt25.genome

Verify and Correct Pedigree

library(tidyverse); library(magrittr);
ped2check_genome<-readRDS(file=here::here("output","ped2check_genome.rds"))
ped2check_genome %<>% 
  select(IID1,IID2,Z0,Z1,Z2,PI_HAT)

ped2check<-read.table(file=here::here("output","ped2genos.txt"),
                      header = F, stringsAsFactors = F) %>% 
  rename(FullSampleName=V1,DamID=V2,SireID=V3)

ped2check %<>% 
  select(FullSampleName,DamID,SireID) %>% 
  inner_join(ped2check_genome %>% 
               rename(FullSampleName=IID1,DamID=IID2) %>% 
               bind_rows(ped2check_genome %>% 
                           rename(FullSampleName=IID2,DamID=IID1))) %>% 
  distinct %>% 
  mutate(ConfirmFemaleParent=case_when(Z0<0.32 & Z1>0.67~"Confirm",
                                       SireID==DamID & PI_HAT>0.6 & Z0<0.3 & Z2>0.32~"Confirm",
                                       TRUE~"Reject")) %>% 
  select(-Z0,-Z1,-Z2,-PI_HAT) %>% 
  inner_join(ped2check_genome %>% 
               rename(FullSampleName=IID1,SireID=IID2) %>% 
               bind_rows(ped2check_genome %>% 
                           rename(FullSampleName=IID2,SireID=IID1))) %>% 
  distinct %>% 
  mutate(ConfirmMaleParent=case_when(Z0<0.32 & Z1>0.67~"Confirm",
                                       SireID==DamID & PI_HAT>0.6 & Z0<0.3 & Z2>0.32~"Confirm",
                                       TRUE~"Reject")) %>% 
  select(-Z0,-Z1,-Z2,-PI_HAT)

ped2check %>% 
  count(ConfirmFemaleParent,ConfirmMaleParent) %>% mutate(Prop=round(n/sum(n),2))

  ConfirmFemaleParent ConfirmMaleParent    n Prop
1             Confirm           Confirm 4259 0.77
2             Confirm            Reject  563 0.10
3              Reject           Confirm  382 0.07
4              Reject            Reject  313 0.06

I’m only interested in families / trios that are confirmed. Remove any without both parents confirmed.

correctedped<-ped2check %>% 
  filter(ConfirmFemaleParent=="Confirm",
         ConfirmMaleParent=="Confirm") %>% 
  select(-contains("Confirm"))

correctedped %>% 
  count(SireID,DamID) %>% arrange(desc(n))

                       SireID                     DamID  n
1           I020129:250090842         I011412:250300323 77
2          MM990477:250090809         I011412:250300323 48
3           I970290:250090804         I940237:250164036 46
4           I011797:250090770         I070004:250164022 45
5           TMEB117:250253666         I961632:250300546 45
6           I940006:250090826         I030075:250300232 41
7           I930007:250090827         I970425:250300465 39
8           I980510:250303662         I980505:250090767 38
9           I071313:250164024         I011412:250300323 37
10          TMEB419:250253865         TMEB419:250253865 35
11          I020233:250300288         I011412:250300323 33
12           I30572:250253643         I980505:250090767 31
13          I010046:250300307         I940237:250164036 30
14          I020540:250300283         I011412:250300323 29
15          I970290:250090804         I950306:250164034 28
16          I930007:250090827         I071313:250164024 26
17          I011412:250300323         I070004:250164022 25
18          I940006:250090826        B9200068:250304480 25
19          M940583:250164037         I010046:250300307 25
20          M980068:250300452        MM964500:250300562 24
21          I010903:250300322         I030060:250090848 23
22          I930007:250090827         I974766:250300468 23
23          TMEB778:250254008         TMEB693:250253991 22
24          I930007:250090827         I000211:250300361 21
25          I940006:250090826        MM964500:250300562 21
26          TMEB419:250253865         I020285:250300276 21
27          I010903:250300322         I970353:250090805 20
28          I010903:250300322         I020129:250090842 19
29          I071313:250164024         I970290:250090804 19
30          I950279:250164033         I063046:250300177 19
31          I980002:250300438         I020285:250300276 19
32          I000355:250300360         I020129:250090842 18
33          I010903:250300322         I972205:250301855 18
34          I030075:250300232         I010046:250300307 18
35         MM970646:250300486         I030060:250090848 18
36          I960963:250300550         I070258:250300140 17
37         MM970806:250164028         I011412:250300323 17
38     2013_0307_20:250161028    2013_10084_6:250164723 16
39          I010046:250300307         M940583:250164037 16
40          I020129:250090842         TMEB419:250253865 16
41          I071313:250164024         I970353:250090805 16
42          I972205:250301855     2013_0088_7:250159759 16
43          I972205:250301855    2013_0343_22:250162550 16
44          I980581:250253626         Z930151:250164040 16
45      2013_0008_6:250162074    2013_0336_23:250162476 15
46    2013_10063_19:250164239    2013_0307_10:250160606 15
47    2013_10063_19:250164239    2013_10084_6:250164723 15
48          I000070:250300358         I961632:250300546 15
49          I000211:250300361         I930134:250164039 15
50         I030055A:250300218         I020540:250300283 15
51          I030075:250300232         I020129:250090842 15
52          I071313:250164024         I020285:250300276 15
53          I930007:250090827         I972205:250301855 15
54          I930134:250164039         Z930151:250164040 15
55          Z930151:250164040        MM970806:250164028 15
56      2013_0108_7:250159843     2013_0307_8:250160604 14
57      2013_0333_3:250162424    2013_10020_4:250164717 14
58          I011371:250090769         I020431:250300292 14
59          I020129:250090842         M980004:250164026 14
60          I071313:250164024        MM970806:250164028 14
61          I930007:250090827     2013_0088_7:250159759 14
62          I970290:250090804        MM970016:250164029 14
63         MM970043:250300482        I030055A:250300218 14
64         MM970043:250300482         I993073:250300423 14
65         MM970043:250300482        MM964500:250300562 14
66         MM970043:250300482         Z930151:250164040 14
67          TMEB419:250253865         I940237:250164036 14
68      2013_0088_7:250159759    2013_0053_15:250162223 13
69     2013_0111_12:250160049     2013_0307_8:250160604 13
70          I000211:250300361        B9200068:250304480 13
71          I930007:250090827         I020285:250300276 13
72          I940006:250090826         I000345:250090783 13
73          I950279:250164033         I070126:250164023 13
74          I972205:250301855    2013_0053_15:250162223 13
75          I972205:250301855        B9200068:250304480 13
76          I974766:250300468         I980196:250164025 13
77         MM970043:250300482         I030060:250090848 13
78  TMS13F1106P0006:250300932     2013_0423_9:250162755 13
79      2013_0108_7:250159843    2013_0307_20:250161028 12
80      2013_0214_4:250160658   2013_10063_19:250164239 12
81     2013_0307_20:250161028    2013_0153_11:250160352 12
82      2013_0307_7:250160603    2013_10309_1:250164479 12
83      2013_0333_3:250162424    2013_0153_11:250160352 12
84          I010046:250300307         I980002:250300438 12
85          I020129:250090842         I950971:250300591 12
86          I020285:250300276         I980002:250300438 12
87         I030055A:250300218         I961632:250300546 12
88         I030060A:250300227    2013_0053_10:250162218 12
89          I051553:250300205         I070004:250164022 12
90          I920429:250164041        B9200061:250304482 12
91          I930134:250164039         I020540:250300283 12
92          I930134:250164039         I070258:250300140 12
93          I940006:250090826         I000211:250300361 12
94          I950306:250164034         I950971:250300591 12
95          I971228:250164027         I011412:250300323 12
96          I972205:250301855     2013_0343_2:250162499 12
97          M980004:250164026         I950971:250300591 12
98         MM970806:250164028         I030060:250090848 12
99         MM990268:250300436         I011412:250300323 12
100         TMEB419:250253865         I972205:250301855 12
101         TMEB419:250253865         I974766:250300468 12
102     2013_0008_6:250162074     2013_0087_2:250159576 11
103     2013_0108_7:250159843    2013_0107_10:250159835 11
104     2013_0108_7:250159843     2013_0436_5:250162760 11
105     2013_0212_2:250159907    2013_10120_1:250164341 11
106    2013_0212_32:250159937     2013_0423_9:250162755 11
107     2013_0307_8:250160604     2013_0212_2:250159907 11
108     2013_0307_8:250160604    2013_10020_4:250164717 11
109     2013_0333_3:250162424     2013_0024_2:250162894 11
110    2013_10059_6:250164095     2013_0436_5:250162760 11
111         I000070:250300358    2013_0053_10:250162218 11
112         I010046:250300307         I010903:250300322 11
113         I010903:250300322         I000211:250300361 11
114        I030055A:250300218         I020431:250300292 11
115         I930007:250090827    2013_0307_16:250160612 11
116         I930007:250090827         I940018:250164035 11
117         I940006:250090826         I000214:250300403 11
118         M980004:250164026         I971228:250164027 11
119         M980068:250300452         I930265:250164038 11
120        MM970043:250300482         I020431:250300292 11
121        MM970806:250164028         I993073:250300423 11
122 TMS13F1106P0006:250300932     2013_0088_8:250159760 11
123         Z930151:250164040         I020540:250300283 11
124     2013_0108_7:250159843     2013_0333_3:250162424 10
125     2013_0108_7:250159843    2013_10084_6:250164723 10
126     2013_0212_2:250159907    2013_0332_42:250161115 10
127     2013_0212_2:250159907    2013_10063_7:250164227 10
128    2013_0212_32:250159937     2013_0436_5:250162760 10
129    2013_0333_17:250162439    2013_0153_11:250160352 10
130    2013_0333_17:250162439 TMS13F1391P0039:250465621 10
131     2013_0333_3:250162424     2013_0160_3:250160398 10
132     2013_0333_3:250162424    2013_0212_55:250159960 10
133     2013_0436_4:250162759   2013_10063_19:250164239 10
134   2013_10063_19:250164239    2013_10303_2:250164467 10
135   2013_10069_24:250164153    2013_0307_16:250160612 10
136    2013_10303_3:250164468     2013_0381_5:250162690 10
137         I010046:250300307         I070004:250164022 10
138         I020285:250300276         I010903:250300322 10
139        I030055A:250300218        MM970806:250164028 10
140         I051740:250300206         I993073:250300423 10
141         I970425:250300465         I993073:250300423 10
142         M980068:250300452         I010903:250300322 10
143         M980068:250300452         I011412:250300323 10
144 TMS14F1292P0015:250304248 TMS14F1229P0002:250303379 10
145         Z930151:250164040         I980196:250164025 10
146     2013_0108_7:250159843    2013_10306_3:250164474  9
147    2013_0212_32:250159937     2013_0050_8:250169056  9
148    2013_0212_32:250159937     2013_0333_3:250162424  9
149    2013_0212_32:250159937    2013_0336_23:250162476  9
150    2013_0212_55:250159960     2013_0154_8:250160392  9
151    2013_0333_17:250162439    2013_10020_4:250164717  9
152    2013_10303_1:250164466    2013_10122_3:250164747  9
153         I020129:250090842         I930007:250090827  9
154        I030060A:250300227    2013_0343_22:250162550  9
155         I920429:250164041         I930134:250164039  9
156         I930007:250090827    2013_10020_1:250164714  9
157         I930007:250090827         I070004:250164022  9
158         I930007:250090827         I970290:250090804  9
159         I940006:250090826         I993073:250300423  9
160          KALESO:250304590         I000211:250300361  9
161          KALESO:250304590         I011412:250300323  9
162        MM970806:250164028         I020431:250300292  9
163        MM970806:250164028        I030055A:250300218  9
164        MM970806:250164028         I930007:250090827  9
165         TMEB419:250253865          I30572:250253643  9
166 TMS13F1106P0006:250300932    2013_10063_9:250164229  9
167     2013_0212_2:250159907    2013_10084_6:250164723  8
168    2013_0307_20:250161028     2013_0109_9:250160030  8
169     2013_0307_4:250160600     2013_0381_5:250162690  8
170     2013_0307_4:250160600    2013_10084_6:250164723  8
171     2013_0307_8:250160604    2013_0333_27:250162449  8
172     2013_0333_3:250162424     2013_0212_2:250159907  8
173     2013_0436_4:250162759     2013_0307_4:250160600  8
174    2013_10020_2:250164715    2013_0307_20:250161028  8
175    2013_10059_6:250164095     2013_0107_6:250159831  8
176         I000211:250300361         I020129:250090842  8
177        I030060A:250300227    2013_0053_15:250162223  8
178        I030060A:250300227     2013_0343_2:250162499  8
179         I030075:250300232         I030007:250300231  8
180         I930007:250090827     2013_0343_2:250162499  8
181         I930007:250090827         I960860:250164032  8
182         I930007:250090827         I971228:250164027  8
183         I930007:250090827         I974580:250300467  8
184         I930134:250164039         I993073:250300423  8
185         I950279:250164033         I960860:250164032  8
186         I972205:250301855    2013_0053_10:250162218  8
187 TMS13F1106P0006:250300932    2013_0008_20:250162088  8
188 TMS13F1106P0006:250300932    2013_0212_55:250159960  8
189 TMS14F1157P0002:250301832 TMS14F1243P0019:250303486  8
190 TMS14F1234P0001:250303393         TMEB693:250253991  8
191         Z930151:250164040         I020131:250300295  8
192         Z930151:250164040         I930134:250164039  8
193     2013_0079_2:250159538   2013_10063_19:250164239  7
194     2013_0108_7:250159843     2013_0028_7:250162328  7
195     2013_0108_7:250159843     2013_0088_8:250159760  7
196     2013_0108_7:250159843    2013_0333_14:250162435  7
197    2013_0154_10:250160394    2013_0212_32:250159937  7
198    2013_0154_10:250160394    2013_0212_58:250159963  7
199     2013_0212_2:250159907    2013_0045_19:250169030  7
200     2013_0212_2:250159907     2013_0079_7:250159543  7
201     2013_0212_2:250159907     2013_0423_9:250162755  7
202    2013_0212_32:250159937    2013_0436_12:250162767  7
203    2013_0307_20:250161028    2013_0107_10:250159835  7
204    2013_0307_20:250161028 TMS13F1106P0006:250300932  7
205    2013_0333_27:250162449     2013_0212_2:250159907  7
206     2013_0333_3:250162424    2013_0212_32:250159937  7
207     2013_0333_3:250162424     2013_0214_4:250160658  7
208   2013_10063_19:250164239     2013_0307_6:250160602  7
209   2013_10063_19:250164239     2013_0381_5:250162690  7
210    2013_10309_1:250164479   2013_10063_19:250164239  7
211         I000070:250300358     2013_0160_5:250160400  7
212         I071313:250164024         I950971:250300591  7
213          I30572:250253643         TMEB419:250253865  7
214         I930007:250090827    2013_0343_22:250162550  7
215         I930007:250090827         I070593:250300163  7
216         I972205:250301855    2013_10020_1:250164714  7
217        MM990268:250300436         I000211:250300361  7
218         TMEB419:250253865    2013_10020_1:250164714  7
219 TMS14F1085P0003:250303128 TMS14F1213P0002:250302239  7
220 TMS14F1240P0005:250303462 TMS14F1283P0002:250303981  7
221 TMS15F1318P0024:250476735 TMS15F1080P0004:250465178  7
222     2013_0008_6:250162074    2013_10086_3:250164329  6
223    2013_0053_15:250162223    2013_0307_16:250160612  6
224     2013_0079_2:250159538    2013_0307_10:250160606  6
225     2013_0088_7:250159759    2013_0307_16:250160612  6
226     2013_0108_7:250159843 TMS13F1106P0006:250300932  6
227    2013_0154_10:250160394    2013_0212_79:250160650  6
228    2013_0212_32:250159937     2013_0109_9:250160030  6
229    2013_0212_55:250159960    2013_0153_11:250160352  6
230    2013_0216_10:250160702     2013_0423_9:250162755  6
231    2013_0307_20:250161028    2013_0333_17:250162439  6
232    2013_0307_20:250161028     2013_0333_3:250162424  6
233    2013_0333_17:250162439    2013_0045_19:250169030  6
234     2013_0333_2:250162423    2013_0153_11:250160352  6
235     2013_0333_3:250162424     2013_0028_7:250162328  6
236     2013_0333_3:250162424    2013_0212_79:250160650  6
237     2013_0333_3:250162424    2013_10309_1:250164479  6
238    2013_10084_6:250164723     2013_0307_8:250160604  6
239    2013_10122_3:250164747   2013_10063_19:250164239  6
240         I000355:250300360         I030060:250090848  6
241         I020129:250090842        MM964500:250300562  6
242         I051740:250300206         I000211:250300361  6
243         I930265:250164038         I030060:250090848  6
244         I940006:250090826         I960869:250300548  6
245         I972205:250301855    2013_0307_16:250160612  6
246         I972205:250301855         I070593:250300163  6
247         TMEB419:250253865    2013_0307_16:250160612  6
248         TMEB419:250253865     2013_0343_2:250162499  6
249    TMS13F1227P0119_A19491 TMS14F1284P0001:250304001  6
250 TMS13F1300P0075:250465619     2013_0079_7:250159543  6
251 TMS14F1085P0003:250303128 TMS14F1196P0005:250302110  6
252 TMS14F1176P0006:250301993 TMS14F1174P0011:250301981  6
253 TMS15F1021P0028:250464932 TMS15F1329P0005:250476750  6
254 TMS15F1069P0007:250521086 TMS15F1351P0003:250466280  6
255 TMS15F1132P0013:250475590 TMS15F1153P0009:250465409  6
256     2013_0008_6:250162074     2013_0154_8:250160392  5
257     2013_0008_6:250162074     2013_0333_2:250162423  5
258     2013_0079_2:250159538     2013_0307_6:250160602  5
259     2013_0088_7:250159759    2013_0343_22:250162550  5
260     2013_0108_7:250159843     2013_0107_6:250159831  5
261    2013_0111_12:250160049    2013_10063_9:250164229  5
262    2013_0154_10:250160394     2013_0212_2:250159907  5
263    2013_0154_10:250160394    2013_0333_14:250162435  5
264     2013_0212_2:250159907     2013_0079_5:250159541  5
265     2013_0212_2:250159907     2013_0333_2:250162423  5
266     2013_0212_2:250159907     2013_0333_3:250162424  5
267    2013_0212_32:250159937    2013_10120_1:250164341  5
268    2013_0212_55:250159960    2013_10084_6:250164723  5
269     2013_0212_7:250159912   2013_10063_19:250164239  5
270    2013_0214_14:250160668    2013_0008_20:250162088  5
271    2013_0307_20:250161028    2013_0212_55:250159960  5
272    2013_0307_20:250161028 TMS13F1391P0039:250465621  5
273     2013_0307_4:250160600    2013_0214_14:250160668  5
274     2013_0307_8:250160604    2013_0332_42:250161115  5
275     2013_0333_3:250162424     2013_0087_2:250159576  5
276     2013_0333_3:250162424    2013_0332_42:250161115  5
277    2013_10020_2:250164715 TMS13F1106P0006:250300932  5
278   2013_10063_19:250164239    2013_10124_2:250164352  5
279    2013_10303_1:250164466     2013_0381_5:250162690  5
280    2013_10303_2:250164467     2013_0381_5:250162690  5
281    2013_10303_2:250164467    2013_10084_6:250164723  5
282    2013_10303_3:250164468    2013_10084_6:250164723  5
283         I000350:250300359         I070004:250164022  5
284         I020129:250090842         I971149:250300466  5
285         I930007:250090827    2013_0053_10:250162218  5
286         I970425:250300465         I010903:250300322  5
287         I972205:250301855    2013_10122_5:250164749  5
288         M940583:250164037         I030060:250090848  5
289         M980068:250300452         I996016:250090791  5
290         TMEB419:250253865    2013_0053_10:250162218  5
291         TMEB419:250253865     2013_0088_7:250159759  5
292         TMEB419:250253865        MM965280:250300556  5
293 TMS14F1085P0003:250303128 TMS14F1213P0007:250302244  5
294 TMS14F1113P0002:250301450 TMS14F1283P0008:250303987  5
295 TMS14F1138P0005:250301674 TMS14F1240P0005:250303462  5
296 TMS14F1138P0005:250301674 TMS14F1244P0006:250303493  5
297 TMS14F1241P0002:250303465 TMS14F1213P0007:250302244  5
298 TMS14F1284P0001:250304001     2013_0160_5:250160400  5
299 TMS15F1153P0009:250465409 TMS15F1092P0016:250465193  5
300 TMS15F1177P0004:250476294 TMS15F1154P0002:250518934  5
301 TMS15F1398P0008:250466574 TMS15F1079P0025:250465175  5
302         Z930151:250164040         I030060:250090848  5
303     2013_0008_6:250162074    2013_10124_2:250164352  4
304     2013_0079_2:250159538     2013_0307_4:250160600  4
305     2013_0108_7:250159843    2013_0307_11:250160607  4
306    2013_0154_10:250160394     2013_0107_8:250159833  4
307    2013_0154_10:250160394    2013_0202_46:250160176  4
308    2013_0154_10:250160394    2013_0216_26:250160718  4
309     2013_0212_2:250159907   2013_10145_11:250164626  4
310    2013_0212_32:250159937     2013_0107_6:250159831  4
311    2013_0212_32:250159937    2013_0111_12:250160049  4
312    2013_0212_32:250159937    2013_0153_11:250160352  4
313    2013_0212_55:250159960     2013_0381_5:250162690  4
314    2013_0212_55:250159960     2013_0420_6:250162738  4
315     2013_0212_7:250159912    2013_10084_6:250164723  4
316    2013_0214_29:250160683     2013_0107_8:250159833  4
317    2013_0214_29:250160683    2013_0307_20:250161028  4
318    2013_0216_10:250160702     2013_0324_2:250161035  4
319    2013_0307_11:250160607    2013_10122_3:250164747  4
320    2013_0307_20:250161028     2013_0324_2:250161035  4
321     2013_0307_8:250160604     2013_0088_8:250159760  4
322     2013_0307_8:250160604    2013_0212_55:250159960  4
323    2013_0332_27:250161100    2013_10122_3:250164747  4
324    2013_0333_17:250162439    2013_0332_42:250161115  4
325    2013_0333_17:250162439    2013_0336_23:250162476  4
326    2013_0333_17:250162439    2013_10084_6:250164723  4
327     2013_0333_3:250162424     2013_0108_7:250159843  4
328    2013_10020_2:250164715    2013_10303_1:250164466  4
329    2013_10084_6:250164723     2013_0212_2:250159907  4
330    2013_10084_6:250164723    2013_0212_79:250160650  4
331    2013_10122_3:250164747     2013_0381_5:250162690  4
332    2013_10303_2:250164467    2013_10124_2:250164352  4
333    2013_10306_3:250164474    2013_0008_20:250162088  4
334         I000070:250300358    2013_0343_22:250162550  4
335         I011797:250090770         I011368:250300318  4
336        I030060A:250300227         I090516:250099187  4
337         I974766:250300468         I940018:250164035  4
338         I980002:250300438         I030075:250300232  4
339 TMS13F1106P0006:250300932     2013_0212_2:250159907  4
340 TMS13F1106P0006:250300932    2013_0212_79:250160650  4
341 TMS13F1106P0006:250300932    2013_0307_20:250161028  4
342 TMS14F1091P0008:250303196 TMS14F1229P0004:250303381  4
343 TMS14F1113P0002:250301450 TMS14F1174P0011:250301981  4
344 TMS14F1138P0005:250301674 TMS14F1122P0003:250301540  4
345 TMS14F1138P0005:250301674 TMS14F1189P0001:250302072  4
346 TMS14F1138P0005:250301674 TMS14F1283P0002:250303981  4
347 TMS14F1166P0002:250301867 TMS14F1154P0001:250301818  4
348 TMS14F1166P0002:250301867 TMS14F1284P0001:250304001  4
349 TMS14F1176P0006:250301993 TMS14F1085P0003:250303128  4
350 TMS14F1240P0005:250303462 TMS14F1138P0005:250301674  4
351 TMS14F1284P0001:250304001 TMS14F1201P0003:250302135  4
352 TMS15F1021P0028:250464932 TMS15F1159P0006:250465430  4
353 TMS15F1132P0013:250475590 TMS15F1244P0004:250465827  4
354 TMS15F1132P0013:250475590 TMS15F1300P0002:250476689  4
355 TMS15F1177P0004:250476294 TMS15F1130P0007:250465327  4
356 TMS15F1310P0019:250467021 TMS15F1024P0006:250464990  4
357 TMS15F1326P0004:250467063 TMS15F1072P0006:250521114  4
358 TMS15F1367P0001:250475193 TMS15F1124P0001:250465316  4
359 TMS15F1398P0008:250466574 TMS15F1072P0012:250521118  4
360     2013_0050_8:250169056    2013_0307_11:250160607  3
361     2013_0079_2:250159538     2013_0212_7:250159912  3
362     2013_0079_2:250159538    2013_10303_1:250164466  3
363     2013_0108_7:250159843     2013_0087_2:250159576  3
364    2013_0111_12:250160049    2013_0212_55:250159960  3
365     2013_0212_2:250159907     2013_0160_9:250160405  3
366     2013_0212_2:250159907    2013_0333_14:250162435  3
367    2013_0212_32:250159937     2013_0160_9:250160405  3
368    2013_0212_32:250159937    2013_0332_45:250161118  3
369    2013_0212_32:250159937 TMS13F1391P0039:250465621  3
370    2013_0212_55:250159960    2013_10020_4:250164717  3
371    2013_0212_55:250159960    2013_10063_9:250164229  3
372    2013_0212_55:250159960 TMS13F1106P0006:250300932  3
373     2013_0212_7:250159912    2013_10122_3:250164747  3
374    2013_0216_10:250160702     2013_0088_8:250159760  3
375     2013_0307_4:250160600    2013_0332_27:250161100  3
376     2013_0307_4:250160600    2013_10122_3:250164747  3
377     2013_0307_8:250160604    2013_10020_2:250164715  3
378     2013_0307_8:250160604    2013_10063_9:250164229  3
379     2013_0307_8:250160604   2013_10145_23:250164638  3
380    2013_0332_27:250161100    2013_0307_11:250160607  3
381     2013_0333_2:250162423    2013_10020_2:250164715  3
382     2013_0333_3:250162424     2013_0153_7:250160348  3
383     2013_0333_3:250162424     2013_0154_8:250160392  3
384     2013_0381_5:250162690     2013_0307_4:250160600  3
385     2013_0381_5:250162690   2013_10063_19:250164239  3
386    2013_10020_2:250164715     2013_0107_6:250159831  3
387    2013_10020_2:250164715    2013_0212_79:250160650  3
388    2013_10059_6:250164095     2013_0107_8:250159833  3
389   2013_10063_19:250164239     2013_0050_8:250169056  3
390   2013_10063_19:250164239    2013_10303_3:250164468  3
391    2013_10084_6:250164723    2013_0307_20:250161028  3
392    2013_10084_6:250164723     2013_0307_4:250160600  3
393    2013_10122_3:250164747    2013_10084_6:250164723  3
394    2013_10303_1:250164466     2013_0050_8:250169056  3
395         I000070:250300358    2013_0307_16:250160612  3
396         I020129:250090842         Z930151:250164040  3
397         I020540:250300283         I930265:250164038  3
398         I930134:250164039        MM990268:250300436  3
399         I950306:250164034        MM990477:250090809  3
400         I960023:250164030         I020431:250300292  3
401         TMEB419:250253865    2013_0053_15:250162223  3
402         TMEB419:250253865     2013_0160_5:250160400  3
403         TMEB419:250253865         I980505:250090767  3
404         TMEB693:250253991         I090516:250099187  3
405 TMS13F1106P0006:250300932     2013_0307_8:250160604  3
406 TMS14F1085P0003:250303128 TMS14F1196P0001:250302106  3
407 TMS14F1113P0002:250301450 TMS14F1091P0009:250303197  3
408 TMS14F1174P0011:250301981 TMS14F1283P0013:250303992  3
409 TMS14F1176P0010:250301997 TMS14F1283P0002:250303981  3
410 TMS14F1195P0008:250302099 TMS14F1107P0004:250301360  3
411 TMS14F1233P0003:250303390 TMS14F1284P0001:250304001  3
412 TMS14F1240P0005:250303462 TMS14F1153P0003:250301810  3
413 TMS14F1240P0005:250303462 TMS14F1283P0008:250303987  3
414 TMS14F1284P0001:250304001 TMS14F1244P0006:250303493  3
415 TMS14F1292P0010:250304243 TMS14F1154P0001:250301818  3
416 TMS15F1153P0009:250465409 TMS15F1100P0005:250465254  3
417 TMS15F1177P0004:250476294 TMS15F1130P0012:250475583  3
418 TMS15F1177P0004:250476294 TMS15F1132P0013:250475590  3
419 TMS15F1305P0021:250476698 TMS15F1025P0001:250464993  3
420 TMS15F1351P0003:250466280 TMS15F1124P0001:250465316  3
421     2013_0008_6:250162074     2013_0028_7:250162328  2
422     2013_0008_6:250162074     2013_0109_9:250160030  2
423     2013_0008_6:250162074    2013_0214_14:250160668  2
424     2013_0008_6:250162074     2013_0307_4:250160600  2
425    2013_0053_15:250162223    2013_0053_10:250162218  2
426     2013_0079_2:250159538    2013_10303_2:250164467  2
427     2013_0088_8:250159760    2013_10122_3:250164747  2
428     2013_0108_7:250159843     2013_0079_2:250159538  2
429     2013_0108_7:250159843    2013_0332_42:250161115  2
430    2013_0111_12:250160049     2013_0307_4:250160600  2
431    2013_0111_12:250160049    2013_10306_3:250164474  2
432     2013_0153_7:250160348     2013_0107_8:250159833  2
433    2013_0154_10:250160394    2013_0212_55:250159960  2
434    2013_0154_10:250160394     2013_0333_2:250162423  2
435    2013_0154_10:250160394    2013_0333_27:250162449  2
436     2013_0212_2:250159907   2013_10034_19:250164218  2
437    2013_0212_32:250159937     2013_0024_2:250162894  2
438    2013_0212_32:250159937    2013_0045_19:250169030  2
439    2013_0212_32:250159937     2013_0333_2:250162423  2
440    2013_0212_32:250159937    2013_10020_4:250164717  2
441    2013_0212_32:250159937 TMS13F1101P0007:250301198  2
442     2013_0212_7:250159912     2013_0050_8:250169056  2
443     2013_0212_7:250159912    2013_0087_14:250159588  2
444    2013_0216_10:250160702    2013_0333_17:250162439  2
445    2013_0216_10:250160702     2013_0436_6:250162761  2
446    2013_0307_11:250160607   2013_10063_19:250164239  2
447    2013_0307_11:250160607    2013_10084_6:250164723  2
448    2013_0307_16:250160612    2013_0053_10:250162218  2
449    2013_0307_20:250161028     2013_0024_2:250162894  2
450    2013_0307_20:250161028     2013_0028_7:250162328  2
451    2013_0307_20:250161028     2013_0079_7:250159543  2
452    2013_0307_20:250161028    2013_0336_23:250162476  2
453    2013_0307_20:250161028 TMS13F1101P0007:250301198  2
454     2013_0307_4:250160600     2013_0050_8:250169056  2
455     2013_0307_6:250160602   2013_10063_19:250164239  2
456     2013_0307_6:250160602    2013_10084_6:250164723  2
457     2013_0307_7:250160603        I030060A:250300227  2
458     2013_0307_8:250160604    2013_0214_14:250160668  2
459    2013_0333_10:250162431     2013_0307_7:250160603  2
460    2013_0333_27:250162449    2013_10122_3:250164747  2
461     2013_0333_3:250162424     2013_0154_5:250160358  2
462     2013_0343_2:250162499    2013_0307_16:250160612  2
463     2013_0436_4:250162759     2013_0160_3:250160398  2
464   2013_10063_19:250164239    2013_0307_11:250160607  2
465   2013_10063_19:250164239     2013_0307_4:250160600  2
466   2013_10063_19:250164239    2013_0332_27:250161100  2
467   2013_10063_19:250164239     2013_0436_4:250162759  2
468   2013_10069_24:250164153    2013_0343_22:250162550  2
469    2013_10084_3:250164720    2013_0214_14:250160668  2
470    2013_10084_6:250164723    2013_10303_1:250164466  2
471    2013_10122_5:250164749    2013_10020_1:250164714  2
472    2013_10303_1:250164466     2013_0436_4:250162759  2
473    2013_10303_1:250164466    2013_10084_6:250164723  2
474    2013_10303_2:250164467     2013_0214_4:250160658  2
475    2013_10303_2:250164467   2013_10063_19:250164239  2
476    2013_10303_2:250164467    2013_10309_1:250164479  2
477    2013_10303_3:250164468    2013_10124_2:250164352  2
478         I000070:250300358 TMS14F1201P0003:250302135  2
479         I000203:250300407         I940018:250164035  2
480         I011368:250300318         I070593:250300163  2
481         I011797:250090770         I070593:250300163  2
482        I030055A:250300218         I930265:250164038  2
483         I030060:250090848    2013_0053_10:250162218  2
484         I070004:250164022        MM990268:250300436  2
485         I930007:250090827   2013_10063_13:250164233  2
486         I930007:250090827         I011412:250300323  2
487         I930007:250090827         I090516:250099187  2
488         I940263:250300608         I940561:250090825  2
489         I972205:250301855         I011797:250090770  2
490           TMEB1:250253593          I91934:250304625  2
491         TMEB419:250253865    2013_0343_22:250162550  2
492           TMEB7:250253599     2013_0160_5:250160400  2
493 TMS13F1106P0006:250300932    2013_0212_58:250159963  2
494 TMS14F1063P0003:250302894 TMS14F1154P0001:250301818  2
495 TMS14F1113P0002:250301450 TMS14F1213P0007:250302244  2
496 TMS14F1157P0002:250301832 TMS14F1189P0001:250302072  2
497 TMS14F1166P0002:250301867 TMS14F1107P0004:250301360  2
498 TMS14F1166P0002:250301867 TMS14F1169P0001:250301880  2
499 TMS14F1174P0011:250301981 TMS14F1153P0003:250301810  2
500 TMS14F1174P0011:250301981 TMS14F1229P0004:250303381  2
501 TMS14F1174P0011:250301981 TMS14F1283P0002:250303981  2
502 TMS14F1176P0006:250301993 TMS14F1091P0008:250303196  2
503 TMS14F1176P0006:250301993 TMS14F1138P0005:250301674  2
504 TMS14F1176P0006:250301993 TMS14F1222P0003:250303322  2
505 TMS14F1240P0004:250303461 TMS14F1283P0015:250303994  2
506 TMS14F1240P0005:250303462 TMS14F1174P0011:250301981  2
507 TMS14F1240P0005:250303462 TMS14F1276P0005:250303833  2
508 TMS14F1240P0005:250303462 TMS14F1283P0013:250303992  2
509 TMS14F1240P0005:250303462 TMS14F1283P0015:250303994  2
510 TMS14F1241P0002:250303465 TMS14F1107P0004:250301360  2
511 TMS14F1247P0007:250303518 TMS14F1229P0004:250303381  2
512 TMS14F1288P0001:250304117 TMS14F1091P0009:250303197  2
513 TMS14F1292P0010:250304243 TMS14F1154P0002:250301819  2
514 TMS15F1069P0007:250521086 TMS15F1333P0001:250467074  2
515 TMS15F1132P0013:250475590 TMS15F1100P0005:250465254  2
516 TMS15F1132P0013:250475590 TMS15F1154P0015:250518942  2
517 TMS15F1132P0013:250475590 TMS15F1234P0001:250465795  2
518 TMS15F1153P0009:250465409 TMS15F1109P0003:250465275  2
519 TMS15F1153P0009:250465409 TMS15F1130P0012:250475583  2
520 TMS15F1156P0014:250518954 TMS15F1072P0031:250521122  2
521 TMS15F1156P0014:250518954 TMS15F1080P0004:250465178  2
522 TMS15F1156P0014:250518954 TMS15F1104P0001:250465265  2
523 TMS15F1156P0014:250518954 TMS15F1109P0003:250465275  2
524 TMS15F1159P0001:250518960 TMS15F1276P0003:250465968  2
525 TMS15F1159P0001:250518960 TMS15F1324P0004:250476746  2
526 TMS15F1159P0001:250518960 TMS15F1326P0004:250467063  2
527 TMS15F1177P0004:250476294 TMS15F1132P0001:250465369  2
528 TMS15F1195P0009:250465561 TMS15F1103P0006:250465263  2
529 TMS15F1318P0009:250476726 TMS15F1103P0006:250465263  2
530 TMS15F1326P0004:250467063 TMS15F1160P0010:250518971  2
531 TMS15F1396P0004:250466562 TMS15F1130P0012:250475583  2
532 TMS15F1396P0004:250466562 TMS15F1153P0009:250465409  2
533 TMS15F1397P0001:250466568 TMS15F1103P0006:250465263  2
534 TMS15F1398P0008:250466574 TMS15F1124P0001:250465316  2
535 TMS15F1398P0008:250466574 TMS15F1130P0002:250475578  2
536    2013_0003_16:250162068     2013_0050_8:250169056  1
537     2013_0008_6:250162074     2013_0079_7:250159543  1
538     2013_0008_6:250162074    2013_0111_12:250160049  1
539     2013_0008_6:250162074     2013_0160_3:250160398  1
540     2013_0008_6:250162074     2013_0212_2:250159907  1
541     2013_0008_6:250162074    2013_0212_58:250159963  1
542     2013_0008_6:250162074   2013_10145_11:250164626  1
543     2013_0008_6:250162074 TMS13F1391P0039:250465621  1
544     2013_0050_8:250169056   2013_10063_19:250164239  1
545     2013_0088_7:250159759    2013_10020_1:250164714  1
546     2013_0108_7:250159843    2013_0154_10:250160394  1
547     2013_0108_7:250159843    2013_0333_17:250162439  1
548     2013_0108_7:250159843     2013_0436_6:250162761  1
549    2013_0111_12:250160049     2013_0107_8:250159833  1
550    2013_0154_10:250160394    2013_0154_10:250160394  1
551    2013_0154_10:250160394    2013_0436_12:250162767  1
552    2013_0202_46:250160176     2013_0107_6:250159831  1
553    2013_0202_46:250160176     2013_0307_4:250160600  1
554     2013_0212_2:250159907     2013_0109_9:250160030  1
555     2013_0212_2:250159907    2013_0253_11:250160418  1
556    2013_0212_32:250159937     2013_0153_7:250160348  1
557    2013_0212_32:250159937     2013_0154_5:250160358  1
558    2013_0212_32:250159937    2013_10063_7:250164227  1
559    2013_0212_32:250159937    2013_10122_3:250164747  1
560    2013_0212_32:250159937    2013_10309_1:250164479  1
561    2013_0212_55:250159960    2013_0008_20:250162088  1
562    2013_0212_55:250159960     2013_0153_7:250160348  1
563    2013_0212_55:250159960     2013_0333_2:250162423  1
564    2013_0212_58:250159963    2013_0332_42:250161115  1
565     2013_0212_7:250159912   2013_10064_25:250164276  1
566    2013_0216_10:250160702 TMS13F1106P0006:250300932  1
567     2013_0216_6:250160698     2013_0107_4:250159829  1
568    2013_0307_10:250160606    2013_0087_14:250159588  1
569    2013_0307_11:250160607    2013_0332_42:250161115  1
570    2013_0307_11:250160607    2013_0333_10:250162431  1
571    2013_0307_12:250160608     2013_0050_8:250169056  1
572    2013_0307_20:250161028    2013_0111_12:250160049  1
573    2013_0307_20:250161028    2013_0154_10:250160394  1
574    2013_0307_20:250161028    2013_0212_61:250159966  1
575    2013_0307_20:250161028    2013_0333_27:250162449  1
576    2013_0307_20:250161028   2013_10063_19:250164239  1
577    2013_0307_23:250161031    2013_0332_42:250161115  1
578     2013_0307_8:250160604    2013_10084_6:250164723  1
579     2013_0333_2:250162423   2013_10145_23:250164638  1
580    2013_0333_27:250162449    2013_0214_14:250160668  1
581    2013_0333_27:250162449    2013_0214_29:250160683  1
582    2013_0333_27:250162449    2013_0332_42:250161115  1
583     2013_0333_3:250162424    2013_0212_58:250159963  1
584     2013_0333_3:250162424    2013_0214_14:250160668  1
585     2013_0333_3:250162424    2013_0214_29:250160683  1
586     2013_0333_3:250162424    2013_0216_28:250160720  1
587     2013_0343_2:250162499     2013_0088_7:250159759  1
588    2013_0343_22:250162550    2013_0053_15:250162223  1
589    2013_0343_22:250162550    2013_0307_16:250160612  1
590     2013_0381_5:250162690    2013_10303_2:250164467  1
591    2013_0436_12:250162767    2013_0212_55:250159960  1
592    2013_10020_2:250164715     2013_0324_2:250161035  1
593   2013_10034_19:250164218    2013_0107_10:250159835  1
594   2013_10063_19:250164239     2013_0307_7:250160603  1
595   2013_10063_19:250164239    2013_0333_10:250162431  1
596   2013_10063_19:250164239   2013_10064_25:250164276  1
597   2013_10063_19:250164239    2013_10309_1:250164479  1
598    2013_10084_3:250164720     2013_0107_6:250159831  1
599    2013_10084_6:250164723     2013_0307_6:250160602  1
600    2013_10122_3:250164747     2013_0214_4:250160658  1
601    2013_10122_3:250164747    2013_0307_10:250160606  1
602    2013_10122_3:250164747     2013_0436_4:250162759  1
603    2013_10122_3:250164747    2013_10303_2:250164467  1
604    2013_10122_3:250164747    2013_10309_1:250164479  1
605    2013_10122_5:250164749    2013_0343_22:250162550  1
606    2013_10122_5:250164749   2013_10063_13:250164233  1
607    2013_10303_1:250164466    2013_0212_55:250159960  1
608    2013_10303_1:250164466    2013_0333_10:250162431  1
609    2013_10303_1:250164466    2013_0333_17:250162439  1
610    2013_10303_1:250164466    2013_10124_2:250164352  1
611    2013_10303_1:250164466    2013_10309_1:250164479  1
612    2013_10303_2:250164467     2013_0050_8:250169056  1
613    2013_10303_2:250164467    2013_0087_14:250159588  1
614    2013_10303_2:250164467   2013_10064_25:250164276  1
615    2013_10303_3:250164468    2013_0332_27:250161100  1
616    2013_10303_3:250164468     2013_0339_9:250162492  1
617    2013_10303_3:250164468   2013_10063_19:250164239  1
618    2013_10306_3:250164474    2013_0332_42:250161115  1
619    2013_10306_3:250164474 TMS13F1391P0039:250465621  1
620    2013_10309_1:250164479    2013_0307_11:250160607  1
621    2013_10309_1:250164479     2013_0307_6:250160602  1
622         I000017:250300396         I070258:250300140  1
623         I000070:250300358    2013_0053_15:250162223  1
624         I011335:250300345         I011371:250090769  1
625         I011368:250300318         I011412:250300323  1
626         I011797:250090770    2013_0053_10:250162218  1
627         I030060:250090848   2013_10377_18:250164522  1
628        I030060A:250300227    2013_10020_1:250164714  1
629         I070004:250164022         I070004:250164022  1
630         I090581:250099170         TMEB693:250253991  1
631        I9102325:250304510        I9102325:250304510  1
632          I91934:250304625           TMEB1:250253593  1
633          I91934:250304625           TMEB9:250253601  1
634         I930007:250090827    2013_0053_15:250162223  1
635         I930007:250090827    2013_10122_5:250164749  1
636         I940006:250090826         I960557:250300551  1
637         I940239:250300602          I91934:250304625  1
638         I940330:250090830         I011663:250300298  1
639         I940330:250090830         I950379:250300567  1
640         I940561:250090825         I950971:250300591  1
641         I950379:250300567        I8902195:250304523  1
642         I972205:250301855         TMEB419:250253865  1
643         I974779:250300473         I980002:250300438  1
644         I992123:250300419         I991702:250090772  1
645         I993073:250300423         I011412:250300323  1
646        MM970646:250300486         I930265:250164038  1
647           TMEB1:250253593       I4_2_1425:250304632  1
648         TMEB117:250253666         I011412:250300323  1
649         TMEB117:250253666         I950379:250300567  1
650         TMEB419:250253865   2013_10063_13:250164233  1
651         TMEB419:250253865    2013_10122_5:250164749  1
652         TMEB419:250253865        MM990477:250090809  1
653         TMEB693:250253991         TMEB693:250253991  1
654           TMEB9:250253601          I30572:250253643  1
655 TMS13F1106P0006:250300932    2013_0212_72:250159977  1
656 TMS13F1106P0006:250300932    2013_0214_29:250160683  1
657 TMS13F1106P0006:250300932    2013_0216_15:250160707  1
658 TMS13F1106P0006:250300932    2013_0216_26:250160718  1
659    TMS13F1227P0119_A19491    2013_0053_15:250162223  1
660 TMS14F1063P0003:250302894 TMS14F1154P0004:250301821  1
661 TMS14F1063P0003:250302894 TMS14F1157P0002:250301832  1
662 TMS14F1113P0002:250301450 TMS14F1138P0005:250301674  1
663 TMS14F1113P0002:250301450 TMS14F1157P0002:250301832  1
664 TMS14F1113P0002:250301450 TMS14F1169P0001:250301880  1
665 TMS14F1113P0002:250301450 TMS14F1247P0007:250303518  1
666 TMS14F1138P0005:250301674 TMS14F1171P0004:250301946  1
667 TMS14F1138P0005:250301674 TMS14F1228P0013:250303377  1
668 TMS14F1157P0002:250301832 TMS14F1244P0006:250303493  1
669 TMS14F1166P0002:250301867 TMS14F1222P0003:250303322  1
670 TMS14F1166P0002:250301867 TMS14F1229P0004:250303381  1
671 TMS14F1166P0002:250301867 TMS14F1247P0003:250303514  1
672 TMS14F1166P0002:250301867 TMS14F1283P0013:250303992  1
673 TMS14F1174P0011:250301981 TMS14F1176P0010:250301997  1
674 TMS14F1174P0011:250301981 TMS14F1247P0003:250303514  1
675 TMS14F1176P0006:250301993 TMS14F1153P0003:250301810  1
676 TMS14F1176P0006:250301993 TMS14F1247P0007:250303518  1
677 TMS14F1176P0010:250301997 TMS14F1174P0011:250301981  1
678 TMS14F1176P0010:250301997 TMS14F1222P0003:250303322  1
679 TMS14F1195P0008:250302099 TMS14F1122P0003:250301540  1
680 TMS14F1240P0004:250303461 TMS14F1213P0007:250302244  1
681 TMS14F1240P0005:250303462 TMS14F1122P0003:250301540  1
682 TMS14F1240P0005:250303462 TMS14F1213P0007:250302244  1
683 TMS14F1240P0005:250303462 TMS14F1228P0013:250303377  1
684 TMS14F1241P0002:250303465 TMS14F1154P0002:250301819  1
685 TMS14F1256P0002:250303615 TMS14F1283P0002:250303981  1
686 TMS14F1288P0001:250304117 TMS14F1244P0006:250303493  1
687 TMS15F1001P0001:250464861 TMS15F1269P0008:250465951  1
688 TMS15F1021P0028:250464932 TMS15F1305P0017:250466080  1
689 TMS15F1021P0028:250464932 TMS15F1318P0009:250476726  1
690 TMS15F1109P0003:250465275 TMS15F1100P0005:250465254  1
691 TMS15F1132P0003:250465370 TMS15F1021P0002:250464910  1
692 TMS15F1132P0013:250475590 TMS15F1196P0010:250465572  1
693 TMS15F1142P0012:250475597 TMS15F1329P0005:250476750  1
694 TMS15F1153P0009:250465409 TMS15F1021P0002:250464910  1
695 TMS15F1153P0009:250465409 TMS15F1073P0005:250465136  1
696 TMS15F1153P0009:250465409 TMS15F1080P0004:250465178  1
697 TMS15F1153P0009:250465409 TMS15F1393P0006:250466543  1
698 TMS15F1154P0002:250518934 TMS15F1351P0003:250466280  1
699 TMS15F1156P0014:250518954 TMS15F1021P0002:250464910  1
700 TMS15F1156P0014:250518954 TMS15F1072P0005:250465127  1
701 TMS15F1156P0014:250518954 TMS15F1079P0020:250465173  1
702 TMS15F1156P0014:250518954 TMS15F1132P0013:250475590  1
703 TMS15F1159P0001:250518960 TMS15F1318P0022:250476734  1
704 TMS15F1159P0006:250465430         I980505:250090767  1
705 TMS15F1159P0006:250465430 TMS15F1021P0002:250464910  1
706 TMS15F1177P0004:250476294 TMS15F1318P0009:250476726  1
707 TMS15F1196P0010:250465572 TMS15F1153P0009:250465409  1
708 TMS15F1196P0010:250465572 TMS15F1154P0002:250518934  1
709 TMS15F1196P0010:250465572 TMS15F1154P0015:250518942  1
710 TMS15F1196P0010:250465572 TMS15F1156P0014:250518954  1
711 TMS15F1305P0017:250466080 TMS15F1079P0020:250465173  1
712 TMS15F1305P0017:250466080 TMS15F1159P0006:250465430  1
713 TMS15F1305P0017:250466080 TMS15F1329P0005:250476750  1
714 TMS15F1310P0019:250467021 TMS15F1196P0010:250465572  1
715 TMS15F1318P0009:250476726 TMS15F1329P0005:250476750  1
716 TMS15F1318P0024:250476735 TMS15F1153P0009:250465409  1
717 TMS15F1318P0024:250476735 TMS15F1160P0010:250518971  1
718 TMS15F1326P0004:250467063 TMS15F1079P0020:250465173  1
719 TMS15F1326P0004:250467063 TMS15F1195P0010:250465562  1
720 TMS15F1351P0003:250466280 TMS15F1396P0001:250466560  1
721 TMS15F1365P0003:250466326 TMS15F1159P0006:250465430  1
722 TMS15F1367P0001:250475193 TMS15F1021P0003:250464911  1
723 TMS15F1367P0001:250475193 TMS15F1069P0007:250521086  1
724 TMS15F1367P0001:250475193 TMS15F1318P0009:250476726  1
725 TMS15F1367P0001:250475193 TMS15F1326P0004:250467063  1
726 TMS15F1396P0001:250466560 TMS15F1351P0003:250466280  1
727 TMS15F1397P0001:250466568 TMS15F1153P0009:250465409  1
728 TMS15F1398P0008:250466574 TMS15F1130P0007:250465327  1

correctedped %>% 
  count(SireID,DamID) %$% summary(n)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    3.00    5.85    8.00   77.00

correctedped %>% 
  count(SireID,DamID) %>% 
  filter(n>=5) %>% arrange(desc(n)) %$% union(SireID,DamID) %>% 
  tibble(ParentsMoreThanFiveProg=.) %>% 
  mutate(Cohort=NA,
         Cohort=ifelse(grepl("TMS18",ParentsMoreThanFiveProg,ignore.case = T),"TMS18",
                       ifelse(grepl("TMS15",ParentsMoreThanFiveProg,ignore.case = T),"TMS15",
                              ifelse(grepl("TMS14",ParentsMoreThanFiveProg,ignore.case = T),"TMS14",
                                     ifelse(grepl("TMS13|2013_",ParentsMoreThanFiveProg,ignore.case = T),"TMS13","GGetc"))))) %>% 
  count(Cohort, name="ParentsWithLeast5offspring")

# A tibble: 4 × 2
  Cohort ParentsWithLeast5offspring
  <chr>                       <int>
1 GGetc                          79
2 TMS13                          77
3 TMS14                          19
4 TMS15                          13

–> Write verified pedigree

correctedped %>% 
  write.table(.,here::here("output","verified_ped.txt"),
              row.names = F, col.names = T, quote = F)

Next Step

Preprocess data files: Prepare haplotype and dosage matrices, pedigree and BLUPs, genetic map and recombination frequency matrix, for use in predictions.

sessionInfo()

R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] magrittr_2.0.1  forcats_0.5.1   stringr_1.4.0   dplyr_1.0.7    
 [5] purrr_0.3.4     readr_2.0.0     tidyr_1.1.3     tibble_3.1.3   
 [9] ggplot2_3.3.5   tidyverse_1.3.1 workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7        here_1.0.1        lubridate_1.7.10  assertthat_0.2.1 
 [5] rprojroot_2.0.2   digest_0.6.27     utf8_1.2.2        R6_2.5.0         
 [9] cellranger_1.1.0  backports_1.2.1   reprex_2.0.0      evaluate_0.14    
[13] highr_0.9         httr_1.4.2        pillar_1.6.2      rlang_0.4.11     
[17] readxl_1.3.1      rstudioapi_0.13   whisker_0.4       jquerylib_0.1.4  
[21] rmarkdown_2.9     labeling_0.4.2    bit_4.0.4         munsell_0.5.0    
[25] broom_0.7.9       compiler_4.1.0    httpuv_1.6.1      modelr_0.1.8     
[29] xfun_0.24         pkgconfig_2.0.3   htmltools_0.5.1.1 tidyselect_1.1.1 
[33] fansi_0.5.0       crayon_1.4.1      tzdb_0.1.2        dbplyr_2.1.1     
[37] withr_2.4.2       later_1.2.0       grid_4.1.0        jsonlite_1.7.2   
[41] gtable_0.3.0      lifecycle_1.0.0   DBI_1.1.1         git2r_0.28.0     
[45] scales_1.1.1      cli_3.0.1         stringi_1.7.3     vroom_1.5.3      
[49] farver_2.1.0      fs_1.5.0          promises_1.2.0.1  xml2_1.3.2       
[53] bslib_0.2.5.1     ellipsis_0.3.2    generics_0.1.0    vctrs_0.3.8      
[57] tools_4.1.0       bit64_4.0.5       glue_1.4.2        hms_1.1.0        
[61] parallel_4.1.0    yaml_2.2.1        colorspace_2.0-2  rvest_1.0.1      
[65] knitr_1.33        haven_2.4.1       sass_0.4.0

Verify the pedigree entries

Marnin Wolfe

2021-May-12