README.md

Results

Cohort freebayes

Variants of freebayes_good/filtering/freebayes_cohort_filtered_snpEff

SNPs
332565
Indels
18481
Complex variants:
50689
SNPs on protein coding regions:
242660
Indels on protein coding regions:
2570
Missense variants on protein coding regions:
103604 freebayes_good/freebayes_cohort_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
79566
Of which come from Indels:
186
Of which come from complex variants:
17168
Synonymous variants on protein coding regions:
175837 freebayes_good/freebayes_cohort_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
163454
Of which come from Indels:
94
Of which come from complex variants:
11621

Variants of freebayes_good/without_filtering/Deha_nofilter_snpEff

SNPs
332565
Indels
18481
Complex variants:
50689
SNPs on protein coding regions:
242660
Indels on protein coding regions:
2570
Missense variants on protein coding regions:
103604 freebayes_good/without_filtering/Deha_nofilter_snpEff_protcod_missense.vcf
Of which come from SNPs:
79566
Of which come from Indels:
186
Of which come from complex variants:
17168
Synonymous variants on protein coding regions:
175837 freebayes_good/without_filtering/Deha_nofilter_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
163454
Of which come from Indels:
94
Of which come from complex variants:
11621

Individual freebayes

Variants of Individual_freebayes/1001AH_freebayes_individual_filtered_snpEff

SNPs
257858
Indels
13129
Complex variants:
41072
SNPs on protein coding regions:
196909
Indels on protein coding regions:
1665
Missense variants on protein coding regions:
79516 Individual_freebayes/1001AH_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
58512
Of which come from Indels:
32
Of which come from complex variants:
14796
Synonymous variants on protein coding regions:
148091 Individual_freebayes/1001AH_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
137975
Of which come from Indels:
23
Of which come from complex variants:
9755

Variants of Individual_freebayes/1001BC_freebayes_individual_filtered_snpEff

SNPs
259553
Indels
13699
Complex variants:
42160
SNPs on protein coding regions:
196937
Indels on protein coding regions:
1729
Missense variants on protein coding regions:
79638 Individual_freebayes/1001BC_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
58471
Of which come from Indels:
29
Of which come from complex variants:
14891
Synonymous variants on protein coding regions:
148221 Individual_freebayes/1001BC_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
138044
Of which come from Indels:
21
Of which come from complex variants:
9813

Variants of Individual_freebayes/nofilter/1001AH_freebayes_individual_nofilter_snpEff

SNPs
257858
Indels
13129
Complex variants:
41072
SNPs on protein coding regions:
196909
Indels on protein coding regions:
1665
Missense variants on protein coding regions:
79516 Individual_freebayes/nofilter/1001AH_freebayes_individual_nofilter_snpEff_protcod_missense.vcf
Of which come from SNPs:
58512
Of which come from Indels:
32
Of which come from complex variants:
14796
Synonymous variants on protein coding regions:
148091 Individual_freebayes/nofilter/1001AH_freebayes_individual_nofilter_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
137975
Of which come from Indels:
23
Of which come from complex variants:
9755

Variants of Individual_freebayes/nofilter/1001BC_freebayes_individual_nofilter_snpEff

SNPs
259553
Indels
13699
Complex variants:
42160
SNPs on protein coding regions:
196937
Indels on protein coding regions:
1729
Missense variants on protein coding regions:
79638 Individual_freebayes/nofilter/1001BC_freebayes_individual_nofilter_snpEff_protcod_missense.vcf
Of which come from SNPs:
58471
Of which come from Indels:
29
Of which come from complex variants:
14891
Synonymous variants on protein coding regions:
148221 Individual_freebayes/nofilter/1001BC_freebayes_individual_nofilter_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
138044
Of which come from Indels:
21
Of which come from complex variants:
9813

Variants of Individual_freebayes/1002AH_freebayes_individual_filtered_snpEff

SNPs
2004
Indels
123
Complex variants:
237
SNPs on protein coding regions:
1241
Indels on protein coding regions:
18
Missense variants on protein coding regions:
866 Individual_freebayes/1002AH_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
730
Of which come from Indels:
0
Of which come from complex variants:
100
Synonymous variants on protein coding regions:
525 Individual_freebayes/1002AH_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
485
Of which come from Indels:
0
Of which come from complex variants:
39

Variants of Individual_freebayes/1002BC_freebayes_individual_filtered_snpEff

SNPs
1133
Indels
114
Complex variants:
152
SNPs on protein coding regions:
571
Indels on protein coding regions:
16
Missense variants on protein coding regions:
369 Individual_freebayes/1002BC_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
287
Of which come from Indels:
0
Of which come from complex variants:
49
Synonymous variants on protein coding regions:
312 Individual_freebayes/1002BC_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
280
Of which come from Indels:
0
Of which come from complex variants:
30

Variants of Individual_freebayes/1003AH_freebayes_individual_filtered_snpEff

SNPs
256180
Indels
13133
Complex variants:
40445
SNPs on protein coding regions:
195225
Indels on protein coding regions:
1631
Missense variants on protein coding regions:
78684 Individual_freebayes/1003AH_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
58064
Of which come from Indels:
47
Of which come from complex variants:
14511
Synonymous variants on protein coding regions:
146606 Individual_freebayes/1003AH_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
136723
Of which come from Indels:
23
Of which come from complex variants:
9533

Variants of Individual_freebayes/1003BC_freebayes_individual_filtered_snpEff

SNPs
258689
Indels
13740
Complex variants:
41837
SNPs on protein coding regions:
195430
Indels on protein coding regions:
1691
Missense variants on protein coding regions:
78894 Individual_freebayes/1003BC_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
58062
Of which come from Indels:
36
Of which come from complex variants:
14665
Synonymous variants on protein coding regions:
146887 Individual_freebayes/1003BC_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
136940
Of which come from Indels:
26
Of which come from complex variants:
9589

Variants of Individual_freebayes/1004AH_freebayes_individual_filtered_snpEff

SNPs
200815
Indels
8532
Complex variants:
25569
SNPs on protein coding regions:
158690
Indels on protein coding regions:
1181
Missense variants on protein coding regions:
62573 Individual_freebayes/1004AH_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
48057
Of which come from Indels:
26
Of which come from complex variants:
10135
Synonymous variants on protein coding regions:
117458 Individual_freebayes/1004AH_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
110270
Of which come from Indels:
18
Of which come from complex variants:
6923

Variants of Individual_freebayes/1004BC_freebayes_individual_filtered_snpEff

SNPs
204035
Indels
9011
Complex variants:
26194
SNPs on protein coding regions:
160374
Indels on protein coding regions:
1237
Missense variants on protein coding regions:
63174 Individual_freebayes/1004BC_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
48413
Of which come from Indels:
22
Of which come from complex variants:
10296
Synonymous variants on protein coding regions:
118885 Individual_freebayes/1004BC_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
111600
Of which come from Indels:
13
Of which come from complex variants:
7030

Variants of Individual_freebayes/1005AH_freebayes_individual_filtered_snpEff

SNPs
2288
Indels
540
Complex variants:
242
SNPs on protein coding regions:
1430
Indels on protein coding regions:
99
Missense variants on protein coding regions:
1022 Individual_freebayes/1005AH_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
898
Of which come from Indels:
1
Of which come from complex variants:
94
Synonymous variants on protein coding regions:
539 Individual_freebayes/1005AH_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
499
Of which come from Indels:
1
Of which come from complex variants:
39

Variants of Individual_freebayes/1005BC_freebayes_individual_filtered_snpEff

SNPs
1592
Indels
546
Complex variants:
194
SNPs on protein coding regions:
850
Indels on protein coding regions:
104
Missense variants on protein coding regions:
605 Individual_freebayes/1005BC_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
514
Of which come from Indels:
2
Of which come from complex variants:
66
Synonymous variants on protein coding regions:
344 Individual_freebayes/1005BC_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
315
Of which come from Indels:
1
Of which come from complex variants:
28

Variants of Individual_freebayes/1007AH_freebayes_individual_filtered_snpEff

SNPs
12294
Indels
1021
Complex variants:
934
SNPs on protein coding regions:
7641
Indels on protein coding regions:
152
Missense variants on protein coding regions:
4177 Individual_freebayes/1007AH_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
3695
Of which come from Indels:
1
Of which come from complex variants:
340
Synonymous variants on protein coding regions:
4056 Individual_freebayes/1007AH_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
3883
Of which come from Indels:
2
Of which come from complex variants:
166

Variants of Individual_freebayes/1007BC_freebayes_individual_filtered_snpEff

SNPs
11673
Indels
1056
Complex variants:
900
SNPs on protein coding regions:
7016
Indels on protein coding regions:
154
Missense variants on protein coding regions:
3705 Individual_freebayes/1007BC_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
3267
Of which come from Indels:
4
Of which come from complex variants:
299
Synonymous variants on protein coding regions:
3870 Individual_freebayes/1007BC_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
3705
Of which come from Indels:
1
Of which come from complex variants:
161

####Variants of Individual_freebayes/1008AH_freebayes_individual_filtered_snpEff

SNPs
13803
Indels
1201
Complex variants:
1097
SNPs on protein coding regions:
8564
Indels on protein coding regions:
220
Missense variants on protein coding regions:
4712 Individual_freebayes/1008AH_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
4169
Of which come from Indels:
4
Of which come from complex variants:
377
Synonymous variants on protein coding regions:
4493 Individual_freebayes/1008AH_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
4323
Of which come from Indels:
1
Of which come from complex variants:
163

Variants of Individual_freebayes/1008BC_freebayes_individual_filtered_snpEff

SNPs
13160
Indels
1232
Complex variants:
1092
SNPs on protein coding regions:
7908
Indels on protein coding regions:
214
Missense variants on protein coding regions:
4234 Individual_freebayes/1008BC_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
3702
Of which come from Indels:
6
Of which come from complex variants:
362
Synonymous variants on protein coding regions:
4340 Individual_freebayes/1008BC_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
4151
Of which come from Indels:
3
Of which come from complex variants:
179

Variants of Individual_freebayes/1013AH_freebayes_individual_filtered_snpEff

SNPs
12882
Indels
1075
Complex variants:
1116
SNPs on protein coding regions:
8070
Indels on protein coding regions:
185
Missense variants on protein coding regions:
4431 Individual_freebayes/1013AH_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
3867
Of which come from Indels:
2
Of which come from complex variants:
406
Synonymous variants on protein coding regions:
4353 Individual_freebayes/1013AH_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
4144
Of which come from Indels:
5
Of which come from complex variants:
194

Variants of Individual_freebayes/1013BC_freebayes_individual_filtered_snpEff

SNPs
12301
Indels
1080
Complex variants:
1139
SNPs on protein coding regions:
7461
Indels on protein coding regions:
193
Missense variants on protein coding regions:
3990 Individual_freebayes/1013BC_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
3430
Of which come from Indels:
11
Of which come from complex variants:
390
Synonymous variants on protein coding regions:
4212 Individual_freebayes/1013BC_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
3995
Of which come from Indels:
7
Of which come from complex variants:
199

Variants of Individual_freebayes/1014AH_freebayes_individual_filtered_snpEff

SNPs
251615
Indels
12730
Complex variants:
38987
SNPs on protein coding regions:
192887
Indels on protein coding regions:
1667
Missense variants on protein coding regions:
77502 Individual_freebayes/1014AH_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
57401
Of which come from Indels:
29
Of which come from complex variants:
14140
Synonymous variants on protein coding regions:
144687 Individual_freebayes/1014AH_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
135053
Of which come from Indels:
20
Of which come from complex variants:
9305

Variants of Individual_freebayes/1014BC_freebayes_individual_filtered_snpEff

SNPs
254246
Indels
13409
Complex variants:
40653
SNPs on protein coding regions:
193034
Indels on protein coding regions:
1712
Missense variants on protein coding regions:
77780 Individual_freebayes/1014BC_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
57356
Of which come from Indels:
35
Of which come from complex variants:
14384
Synonymous variants on protein coding regions:
144954 Individual_freebayes/1014BC_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
135247
Of which come from Indels:
17
Of which come from complex variants:
9376

Variants of Individual_freebayes/1015AH_freebayes_individual_filtered_snpEff

SNPs
14555
Indels
1269
Complex variants:
1246
SNPs on protein coding regions:
8939
Indels on protein coding regions:
210
Missense variants on protein coding regions:
4872 Individual_freebayes/1015AH_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
4262
Of which come from Indels:
7
Of which come from complex variants:
426
Synonymous variants on protein coding regions:
4806 Individual_freebayes/1015AH_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
4605
Of which come from Indels:
0
Of which come from complex variants:
193

Variants of Individual_freebayes/1015BC_freebayes_individual_filtered_snpEff

SNPs
14119
Indels
1331
Complex variants:
1262
SNPs on protein coding regions:
8407
Indels on protein coding regions:
215
Missense variants on protein coding regions:
4440 Individual_freebayes/1015BC_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
3857
Of which come from Indels:
3
Of which come from complex variants:
401
Synonymous variants on protein coding regions:
4699 Individual_freebayes/1015BC_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
4494
Of which come from Indels:
5
Of which come from complex variants:
191

Variants of Individual_freebayes/1016AH_freebayes_individual_filtered_snpEff

SNPs
259110
Indels
13420
Complex variants:
41559
SNPs on protein coding regions:
197400
Indels on protein coding regions:
1687
Missense variants on protein coding regions:
79767 Individual_freebayes/1016AH_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
58587
Of which come from Indels:
33
Of which come from complex variants:
14931
Synonymous variants on protein coding regions:
148595 Individual_freebayes/1016AH_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
138372
Of which come from Indels:
19
Of which come from complex variants:
9859

Variants of Individual_freebayes/1016BC_freebayes_individual_filtered_snpEff

SNPs
261471
Indels
13937
Complex variants:
42816
SNPs on protein coding regions:
197600
Indels on protein coding regions:
1727
Missense variants on protein coding regions:
80021 Individual_freebayes/1016BC_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
58605
Of which come from Indels:
40
Of which come from complex variants:
15087
Synonymous variants on protein coding regions:
148792 Individual_freebayes/1016BC_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
138546
Of which come from Indels:
25
Of which come from complex variants:
9880

Variants of Individual_freebayes/1019AH_freebayes_individual_filtered_snpEff

SNPs
1917
Indels
109
Complex variants:
177
SNPs on protein coding regions:
1161
Indels on protein coding regions:
12
Missense variants on protein coding regions:
802 Individual_freebayes/1019AH_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
707
Of which come from Indels:
0
Of which come from complex variants:
61
Synonymous variants on protein coding regions:
472 Individual_freebayes/1019AH_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
439
Of which come from Indels:
0
Of which come from complex variants:
32

Variants of Individual_freebayes/1019BC_freebayes_individual_filtered_snpEff

SNPs
1278
Indels
114
Complex variants:
164
SNPs on protein coding regions:
626
Indels on protein coding regions:
13
Missense variants on protein coding regions:
402 Individual_freebayes/1019BC_freebayes_individual_filtered_snpEff_protcod_missense.vcf
Of which come from SNPs:
334
Of which come from Indels:
0
Of which come from complex variants:
44
Synonymous variants on protein coding regions:
310 Individual_freebayes/1019BC_freebayes_individual_filtered_snpEff_protcod_synonymous.vcf
Of which come from SNPs:
283
Of which come from Indels:
0
Of which come from complex variants:
26