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SamGurr committed Dec 9, 2024
1 parent 7bb6b94 commit 8461d96
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Showing 5 changed files with 975 additions and 643 deletions.
54 changes: 27 additions & 27 deletions RAnalysis/Data/Popgen/Parentages/F1_parentage.csv
Original file line number Diff line number Diff line change
@@ -1,27 +1,27 @@
Broodstock_ID,Seqdata_ID_raw,Seqdata_ID,Batch_1,Batch_2,Batch_3,Batch_4,Batch_5,key,Ped
1,adapter_trim.F0-B1,F0-B1,F,F,M,M,M,Pa,Both
2,adapter_trim.F0-B2,F0-B2,F,M,F,M,M,Pa,Both
3,adapter_trim.F0-B3,F0-B3,NA,M,F,NA,F,Pa,Both
4,adapter_trim.F0-B4,F0-B4,F,NA,M,M,M,Pa,Both
5,adapter_trim.F0-B5,F0-B5,M,NA,NA,M,M,Fa,Sire
6,adapter_trim.F0-B6,F0-B6,M,NA,M,NA,NA,Fa,Sire
7,adapter_trim.F0-B7,F0-B7,F,M,M,F,F,Pa,Both
9,adapter_trim.F0-B9,F0-B9,NA,M,M,M,M,Fa,Sire
10,adapter_trim.F0-B10,F0-B10,NA,F,F,NA,F,Mo,Dam
11,adapter_trim.F0-B11,F0-B11,M,M,M,F,F,Pa,Both
12,adapter_trim.F0-B12,F0-B12,NA,NA,NA,NA,NA,NA,NA
13,adapter_trim.F0-B13,F0-B13,F,F,NA,F,NA,Mo,Dam
14,adapter_trim.F0-B14,F0-B14,NA,F,F,F,F,Mo,Dam
15,adapter_trim.F0-B15,F0-B15,NA,NA,NA,M,M,Fa,Sire
16,adapter_trim.F0-B16,F0-B16,NA,F,F,F,F,Mo,Dam
17,adapter_trim.F0-B17,F0-B17,M,NA,M,NA,NA,Fa,Sire
18,adapter_trim.F0-B18,F0-B18,NA,NA,NA,M,M,Fa,Sire
19,adapter_trim.F0-B19,F0-B19,NA,NA,NA,NA,NA,NA,NA
20,adapter_trim.F0-B20,F0-B20,NA,F,NA,F,NA,Mo,Dam
21,adapter_trim.F0-B21,F0-B21,NA,NA,NA,M,M,Fa,Sire
22,adapter_trim.F0-B22,F0-B22,NA,NA,NA,M,M,Fa,Sire
23,adapter_trim.F0-B23,F0-B23,NA,NA,NA,NA,NA,NA,NA
24,adapter_trim.F0-B24,F0-B24,NA,NA,M,M,M,Fa,Sire
25,adapter_trim.F0-B25,F0-B25,M,NA,M,M,M,Fa,Sire
26,adapter_trim.F0-B26,F0-B26,NA,F,NA,F,F,Mo,Dam
27,adapter_trim.F0-B27,F0-B27,NA,NA,F,NA,NA,Mo,Dam
Broodstock_ID,vcf_ID_raw,ID,Batch_1,Batch_2,Batch_3,Batch_4,Batch_5,key,Ped
1,adapter_trim.F0-B1.bam,F0-B1,F,F,M,M,M,Pa,Both
2,adapter_trim.F0-B2.bam,F0-B2,F,M,F,M,M,Pa,Both
3,adapter_trim.F0-B3.bam,F0-B3,NA,M,F,NA,F,Pa,Both
4,adapter_trim.F0-B4.bam,F0-B4,F,NA,M,M,M,Pa,Both
5,adapter_trim.F0-B5.bam,F0-B5,M,NA,NA,M,M,Fa,Sire
6,adapter_trim.F0-B6.bam,F0-B6,M,NA,M,NA,NA,Fa,Sire
7,adapter_trim.F0-B7.bam,F0-B7,F,M,M,F,F,Pa,Both
9,adapter_trim.F0-B9.bam,F0-B9,NA,M,M,M,M,Fa,Sire
10,adapter_trim.F0-B10.bam,F0-B10,NA,F,F,NA,F,Mo,Dam
11,adapter_trim.F0-B11.bam,F0-B11,M,M,M,F,F,Pa,Both
12,adapter_trim.F0-B12.bam,F0-B12,NA,NA,NA,NA,NA,NA,NA
13,adapter_trim.F0-B13.bam,F0-B13,F,F,NA,F,NA,Mo,Dam
14,adapter_trim.F0-B14.bam,F0-B14,NA,F,F,F,F,Mo,Dam
15,adapter_trim.F0-B15.bam,F0-B15,NA,NA,NA,M,M,Fa,Sire
16,adapter_trim.F0-B16.bam,F0-B16,NA,F,F,F,F,Mo,Dam
17,adapter_trim.F0-B17.bam,F0-B17,M,NA,M,NA,NA,Fa,Sire
18,adapter_trim.F0-B18.bam,F0-B18,NA,NA,NA,M,M,Fa,Sire
19,adapter_trim.F0-B19.bam,F0-B19,NA,NA,NA,NA,NA,NA,NA
20,adapter_trim.F0-B20.bam,F0-B20,NA,F,NA,F,NA,Mo,Dam
21,adapter_trim.F0-B21.bam,F0-B21,NA,NA,NA,M,M,Fa,Sire
22,adapter_trim.F0-B22.bam,F0-B22,NA,NA,NA,M,M,Fa,Sire
23,adapter_trim.F0-B23.bam,F0-B23,NA,NA,NA,NA,NA,NA,NA
24,adapter_trim.F0-B24.bam,F0-B24,NA,NA,M,M,M,Fa,Sire
25,adapter_trim.F0-B25.bam,F0-B25,M,NA,M,M,M,Fa,Sire
26,adapter_trim.F0-B26.bam,F0-B26,NA,F,NA,F,F,Mo,Dam
27,adapter_trim.F0-B27.bam,F0-B27,NA,NA,F,NA,NA,Mo,Dam
74 changes: 37 additions & 37 deletions RAnalysis/Data/Popgen/Parentages/F2_parentage.csv
Original file line number Diff line number Diff line change
@@ -1,37 +1,37 @@
Broodstock_ID,Treatment,Seqdata_ID,Batch_1,Batch_2,Batch_3,Batch_4,key,Ped
1,Moderate,F1-B1-pH75,M,NA,NA,M,Fa,Sire
2,Moderate,F1-B2-pH75,M,NA,NA,NA,Fa,Sire
4,Moderate,F1-B4-pH75,NA,M,NA,M,Fa,Sire
5,Moderate,F1-B5-pH75,NA,M,NA,M,Fa,Sire
6,Moderate,F1-B6-pH75,F,NA,NA,F,Mo,Dam
8,Moderate,F1-B8-pH75,NA,NA,M,NA,Fa,Sire
9,Moderate,F1-B9-pH75,NA,M,NA,NA,Fa,Sire
10,Moderate,F1-B10-pH75,NA,F,NA,F,Mo,Dam
11,Moderate,F1-B11-pH75,NA,F,NA,F,Mo,Dam
12,Moderate,F1-B12-pH75,NA,F,NA,NA,Mo,Dam
14,Moderate,F1-B14-pH75,M,NA,NA,M,Fa,Sire
16,Moderate,F1-B16-pH75,NA,NA,F,NA,Mo,Dam
17,Moderate,F1-B17-pH75,F,NA,NA,NA,Mo,Dam
18,Moderate,F1-B18-pH75,NA,NA,F,NA,Mo,Dam
19,Moderate,F1-B19-pH75,NA,NA,F,NA,Mo,Dam
20,Moderate,F1-B20-pH75,NA,NA,M,NA,Fa,Sire
21,Moderate,F1-B21-pH75,F,NA,NA,NA,Mo,Dam
24,Moderate,F1-B24-pH75,NA,NA,M,NA,Fa,Sire
1,Low,F1-B1-pH8,NA,M,NA,M,Fa,Sire
2,Low,F1-B2-pH8,M,NA,NA,NA,Fa,Sire
3,Low,F1-B3-pH8,NA,NA,M,NA,Fa,Sire
4,Low,F1-B4-pH8,M,NA,NA,NA,Fa,Sire
5,Low,F1-B5-pH8,NA,NA,M,NA,Fa,Sire
7,Low,F1-B7-pH8,NA,NA,M,M,Fa,Sire
8,Low,F1-B8-pH8,F,M,NA,NA,Pa,Both
9,Low,F1-B9-pH8,M,NA,NA,M,Fa,Sire
10,Low,F1-B10-pH8,NA,M,NA,NA,Fa,Sire
11,Low,F1-B11-pH8,NA,NA,NA,M,Fa,Sire
15,Low,F1-B15-pH8,F,NA,NA,F,Mo,Dam
17,Low,F1-B17-pH8,F,NA,NA,NA,Mo,Dam
19,Low,F1-B19-pH8,NA,F,NA,NA,Mo,Dam
20,Low,F1-B20-pH8,NA,F,NA,NA,Mo,Dam
21,Low,F1-B21-pH8,NA,F,NA,F,Mo,Dam
22,Low,F1-B22-pH8,NA,NA,F,NA,Mo,Dam
23,Low,F1-B23-pH8,NA,NA,F,F,Mo,Dam
25,Low,F1-B25-pH8,NA,NA,F,NA,Mo,Dam
Broodstock_ID,Treatment,vcf_ID_raw,ID,Batch_1,Batch_2,Batch_3,Batch_4,key,Ped
1,Moderate,adapter_trim.F1-B1-pH75.bam,F1-B1-pH75,M,NA,NA,M,Fa,Sire
2,Moderate,adapter_trim.F1-B2-pH75.bam,F1-B2-pH75,M,NA,NA,NA,Fa,Sire
4,Moderate,adapter_trim.F1-B4-pH75.bam,F1-B4-pH75,NA,M,NA,M,Fa,Sire
5,Moderate,adapter_trim.F1-B5-pH75.bam,F1-B5-pH75,NA,M,NA,M,Fa,Sire
6,Moderate,adapter_trim.F1-B6-pH75.bam,F1-B6-pH75,F,NA,NA,F,Mo,Dam
8,Moderate,adapter_trim.F1-B8-pH75.bam,F1-B8-pH75,NA,NA,M,NA,Fa,Sire
9,Moderate,adapter_trim.F1-B9-pH75.bam,F1-B9-pH75,NA,M,NA,NA,Fa,Sire
10,Moderate,adapter_trim.F1-B10-pH75.bam,F1-B10-pH75,NA,F,NA,F,Mo,Dam
11,Moderate,adapter_trim.F1-B11-pH75.bam,F1-B11-pH75,NA,F,NA,F,Mo,Dam
12,Moderate,adapter_trim.F1-B12-pH75.bam,F1-B12-pH75,NA,F,NA,NA,Mo,Dam
14,Moderate,adapter_trim.F1-B14-pH75.bam,F1-B14-pH75,M,NA,NA,M,Fa,Sire
16,Moderate,adapter_trim.F1-B16-pH75.bam,F1-B16-pH75,NA,NA,F,NA,Mo,Dam
17,Moderate,adapter_trim.F1-B17-pH75.bam,F1-B17-pH75,F,NA,NA,NA,Mo,Dam
18,Moderate,adapter_trim.F1-B18-pH75.bam,F1-B18-pH75,NA,NA,F,NA,Mo,Dam
19,Moderate,adapter_trim.F1-B19-pH75.bam,F1-B19-pH75,NA,NA,F,NA,Mo,Dam
20,Moderate,adapter_trim.F1-B20-pH75.bam,F1-B20-pH75,NA,NA,M,NA,Fa,Sire
21,Moderate,adapter_trim.F1-B21-pH75.bam,F1-B21-pH75,F,NA,NA,NA,Mo,Dam
24,Moderate,adapter_trim.F1-B24-pH75.bam,F1-B24-pH75,NA,NA,M,NA,Fa,Sire
1,Low,adapter_trim.F1-B1-pH8.bam,F1-B1-pH8,NA,M,NA,M,Fa,Sire
2,Low,adapter_trim.F1-B2-pH8.bam,F1-B2-pH8,M,NA,NA,NA,Fa,Sire
3,Low,adapter_trim.F1-B3-pH8.bam,F1-B3-pH8,NA,NA,M,NA,Fa,Sire
4,Low,adapter_trim.F1-B4-pH8.bam,F1-B4-pH8,M,NA,NA,NA,Fa,Sire
5,Low,adapter_trim.F1-B5-pH8.bam,F1-B5-pH8,NA,NA,M,NA,Fa,Sire
7,Low,adapter_trim.F1-B7-pH8.bam,F1-B7-pH8,NA,NA,M,M,Fa,Sire
8,Low,adapter_trim.F1-B8-pH8.bam,F1-B8-pH8,F,M,NA,NA,Pa,Both
9,Low,adapter_trim.F1-B9-pH8.bam,F1-B9-pH8,M,NA,NA,M,Fa,Sire
10,Low,adapter_trim.F1-B10-pH8.bam,F1-B10-pH8,NA,M,NA,NA,Fa,Sire
11,Low,adapter_trim.F1-B11-pH8.bam,F1-B11-pH8,NA,NA,NA,M,Fa,Sire
15,Low,adapter_trim.F1-B15-pH8.bam,F1-B15-pH8,F,NA,NA,F,Mo,Dam
17,Low,adapter_trim.F1-B17-pH8.bam,F1-B17-pH8,F,NA,NA,NA,Mo,Dam
19,Low,adapter_trim.F1-B19-pH8.bam,F1-B19-pH8,NA,F,NA,NA,Mo,Dam
20,Low,adapter_trim.F1-B20-pH8.bam,F1-B20-pH8,NA,F,NA,NA,Mo,Dam
21,Low,adapter_trim.F1-B21-pH8.bam,F1-B21-pH8,NA,F,NA,F,Mo,Dam
22,Low,adapter_trim.F1-B22-pH8.bam,F1-B22-pH8,NA,NA,F,NA,Mo,Dam
23,Low,adapter_trim.F1-B23-pH8.bam,F1-B23-pH8,NA,NA,F,F,Mo,Dam
25,Low,adapter_trim.F1-B25-pH8.bam,F1-B25-pH8,NA,NA,F,NA,Mo,Dam
92 changes: 46 additions & 46 deletions RAnalysis/Data/Popgen/Parentages/F3_parentage.csv
Original file line number Diff line number Diff line change
@@ -1,46 +1,46 @@
Broodstock_ID,Treatment,Seqdata_ID,Batch_1,Batch_2,Batch_3,Batch_4,key,Ped
1,High,F3-B1-pH7,F,M,NA,NA,Pa,Both
2,High,F3-B2-pH7,F,M,NA,NA,Pa,Both
3,High,F3-B3-pH7,M,NA,NA,NA,Fa,Sire
4,High,F3-B4-pH7,M,F,NA,NA,Pa,Both
5,High,F3-B5-pH7,NA,NA,M,NA,Fa,Sire
6,High,F3-B6-pH7,NA,F,NA,NA,Mo,Dam
7,High,F3-B7-pH7,NA,NA,F,NA,Mo,Dam
8,High,F3-B8-pH7,NA,NA,NA,M,Fa,Sire
9,High,F3-B9-pH7,NA,F,NA,NA,Mo,Dam
10,High,F3-B10-pH7,F,NA,M,NA,Pa,Both
12,High,F3-B12-pH7,NA,NA,F,NA,Mo,Dam
15,High,F3-B15-pH7,NA,NA,NA,F,Mo,Dam
16,High,F3-B16-pH7,NA,NA,NA,F,Mo,Dam
18,High,F3-B18-pH7,NA,NA,F,NA,Mo,Dam
19,High,F3-B19-pH7,NA,NA,NA,F,Mo,Dam
25,High,F3-B25-pH7,NA,NA,NA,M,Fa,Sire
1,Moderate,F3-B1-pH75,NA,F,M,NA,Pa,Both
2,Moderate,F3-B2-pH75,F,NA,NA,NA,Mo,Dam
3,Moderate,F3-B3-pH75,NA,NA,NA,F,Mo,Dam
5,Moderate,F3-B5-pH75,NA,F,NA,NA,Mo,Dam
6,Moderate,F3-B6-pH75,NA,NA,F,NA,Mo,Dam
10,Moderate,F3-B10-pH75,NA,NA,M,NA,Fa,Sire
11,Moderate,F3-B11-pH75,F,M,NA,NA,Pa,Both
14,Moderate,F3-B14-pH75,M,F,NA,NA,Pa,Both
16,Moderate,F3-B16-pH75,M,NA,NA,NA,Fa,Sire
17,Moderate,F3-B17-pH75,NA,M,F,NA,Pa,Both
19,Moderate,F3-B19-pH75,F,NA,NA,M,Pa,Both
21,Moderate,F3-B21-pH75,NA,NA,F,NA,Mo,Dam
22,Moderate,F3-B22-pH75,NA,NA,NA,M,Fa,Sire
24,Moderate,F3-B24-pH75,NA,NA,NA,F,Mo,Dam
25,Moderate,F3-B25-pH75,NA,NA,NA,F,Mo,Dam
1,Low,F3-B1-pH8,F,NA,NA,NA,Mo,Dam
2,Low,F3-B2-pH8,F,NA,NA,M,Pa,Both
3,Low,F3-B3-pH8,NA,NA,NA,M,Pa,Both
5,Low,F3-B5-pH8,F,NA,NA,NA,Mo,Dam
6,Low,F3-B6-pH8,NA,M,NA,F,Pa,Both
7,Low,F3-B7-pH8,NA,M,F,NA,Pa,Both
8,Low,F3-B8-pH8,NA,NA,M,F,Pa,Both
10,Low,F3-B10-pH8,NA,F,NA,NA,Mo,Dam
11,Low,F3-B11-pH8,M,NA,NA,NA,Fa,Sire
12,Low,F3-B12-pH8,M,NA,F,NA,Pa,Both
13,Low,F3-B13-pH8,NA,NA,F,NA,Mo,Dam
15,Low,F3-B15-pH8,NA,F,NA,NA,Mo,Dam
16,Low,F3-B16-pH8,NA,NA,M,F,Pa,Both
23,Low,F3-B23-pH8,NA,F,NA,NA,Mo,Dam
Broodstock_ID,Treatment,vcf_ID_raw,ID,Batch_1,Batch_2,Batch_3,Batch_4,key,Ped
1,High,adapter_trim.F3-B1-pH7.bam,F3-B1-pH7,F,M,NA,NA,Pa,Both
2,High,adapter_trim.F3-B2-pH7.bam,F3-B2-pH7,F,M,NA,NA,Pa,Both
3,High,adapter_trim.F3-B3-pH7.bam,F3-B3-pH7,M,NA,NA,NA,Fa,Sire
4,High,adapter_trim.F3-B4-pH7.bam,F3-B4-pH7,M,F,NA,NA,Pa,Both
5,High,adapter_trim.F3-B5-pH7.bam,F3-B5-pH7,NA,NA,M,NA,Fa,Sire
6,High,adapter_trim.F3-B6-pH7.bam,F3-B6-pH7,NA,F,NA,NA,Mo,Dam
7,High,adapter_trim.F3-B7-pH7.bam,F3-B7-pH7,NA,NA,F,NA,Mo,Dam
8,High,adapter_trim.F3-B8-pH7.bam,F3-B8-pH7,NA,NA,NA,M,Fa,Sire
9,High,adapter_trim.F3-B9-pH7.bam,F3-B9-pH7,NA,F,NA,NA,Mo,Dam
10,High,adapter_trim.F3-B10-pH7.bam,F3-B10-pH7,F,NA,M,NA,Pa,Both
12,High,adapter_trim.F3-B12-pH7.bam,F3-B12-pH7,NA,NA,F,NA,Mo,Dam
15,High,adapter_trim.F3-B15-pH7.bam,F3-B15-pH7,NA,NA,NA,F,Mo,Dam
16,High,adapter_trim.F3-B16-pH7.bam,F3-B16-pH7,NA,NA,NA,F,Mo,Dam
18,High,adapter_trim.F3-B18-pH7.bam,F3-B18-pH7,NA,NA,F,NA,Mo,Dam
19,High,adapter_trim.F3-B19-pH7.bam,F3-B19-pH7,NA,NA,NA,F,Mo,Dam
25,High,adapter_trim.F3-B25-pH7.bam,F3-B25-pH7,NA,NA,NA,M,Fa,Sire
1,Moderate,adapter_trim.F3-B1-pH75.bam,F3-B1-pH75,NA,F,M,NA,Pa,Both
2,Moderate,adapter_trim.F3-B2-pH75.bam,F3-B2-pH75,F,NA,NA,NA,Mo,Dam
3,Moderate,adapter_trim.F3-B3-pH75.bam,F3-B3-pH75,NA,NA,NA,F,Mo,Dam
5,Moderate,adapter_trim.F3-B5-pH75.bam,F3-B5-pH75,NA,F,NA,NA,Mo,Dam
6,Moderate,adapter_trim.F3-B6-pH75.bam,F3-B6-pH75,NA,NA,F,NA,Mo,Dam
10,Moderate,adapter_trim.F3-B10-pH75.bam,F3-B10-pH75,NA,NA,M,NA,Fa,Sire
11,Moderate,adapter_trim.F3-B11-pH75.bam,F3-B11-pH75,F,M,NA,NA,Pa,Both
14,Moderate,adapter_trim.F3-B14-pH75.bam,F3-B14-pH75,M,F,NA,NA,Pa,Both
16,Moderate,adapter_trim.F3-B16-pH75.bam,F3-B16-pH75,M,NA,NA,NA,Fa,Sire
17,Moderate,adapter_trim.F3-B17-pH75.bam,F3-B17-pH75,NA,M,F,NA,Pa,Both
19,Moderate,adapter_trim.F3-B19-pH75.bam,F3-B19-pH75,F,NA,NA,M,Pa,Both
21,Moderate,adapter_trim.F3-B21-pH75.bam,F3-B21-pH75,NA,NA,F,NA,Mo,Dam
22,Moderate,adapter_trim.F3-B22-pH75.bam,F3-B22-pH75,NA,NA,NA,M,Fa,Sire
24,Moderate,adapter_trim.F3-B24-pH75.bam,F3-B24-pH75,NA,NA,NA,F,Mo,Dam
25,Moderate,adapter_trim.F3-B25-pH75.bam,F3-B25-pH75,NA,NA,NA,F,Mo,Dam
1,Low,adapter_trim.F3-B1-pH8.bam,F3-B1-pH8,F,NA,NA,NA,Mo,Dam
2,Low,adapter_trim.F3-B2-pH8.bam,F3-B2-pH8,F,NA,NA,M,Pa,Both
3,Low,adapter_trim.F3-B3-pH8.bam,F3-B3-pH8,NA,NA,NA,M,Pa,Both
5,Low,adapter_trim.F3-B5-pH8.bam,F3-B5-pH8,F,NA,NA,NA,Mo,Dam
6,Low,adapter_trim.F3-B6-pH8.bam,F3-B6-pH8,NA,M,NA,F,Pa,Both
7,Low,adapter_trim.F3-B7-pH8.bam,F3-B7-pH8,NA,M,F,NA,Pa,Both
8,Low,adapter_trim.F3-B8-pH8.bam,F3-B8-pH8,NA,NA,M,F,Pa,Both
10,Low,adapter_trim.F3-B10-pH8.bam,F3-B10-pH8,NA,F,NA,NA,Mo,Dam
11,Low,adapter_trim.F3-B11-pH8.bam,F3-B11-pH8,M,NA,NA,NA,Fa,Sire
12,Low,adapter_trim.F3-B12-pH8.bam,F3-B12-pH8,M,NA,F,NA,Pa,Both
13,Low,adapter_trim.F3-B13-pH8.bam,F3-B13-pH8,NA,NA,F,NA,Mo,Dam
15,Low,adapter_trim.F3-B15-pH8.bam,F3-B15-pH8,NA,F,NA,NA,Mo,Dam
16,Low,adapter_trim.F3-B16-pH8.bam,F3-B16-pH8,NA,NA,M,F,Pa,Both
23,Low,adapter_trim.F3-B23-pH8.bam,F3-B23-pH8,NA,F,NA,NA,Mo,Dam
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