/EXTERNAL KNIH/variants/K006242_1_lane_gembs
BACK
SAMPLE K006242_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1205126539 |
694752875 |
57.65 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1205126539 |
100% |
1135858829 |
94.25 % |
69267710 |
5.75 % |
| |
|
|
|
|
|
|
| Passed |
709001479 |
58.83 % |
684758681 |
60.29 % |
24242798 |
3.42 % |
| Filtered |
496125060 |
41.17 % |
451100148 |
39.71 % |
45024912 |
6.35 % |
| |
|
|
|
|
|
|
| q20 |
427552045 |
86.18 % |
412468997 |
91.44 % |
15083048 |
33.50 % |
| q20,qd2 |
51749821 |
10.43 % |
23771056 |
5.27 % |
27978765 |
62.14 % |
| qd2 |
9321815 |
1.88 % |
7753685 |
1.72 % |
1568130 |
3.48 % |
| q20,mq40 |
4800607 |
0.97 % |
4665396 |
1.03 % |
135211 |
0.30 % |
| q20,qd2,mq40 |
2114114 |
0.43 % |
2025123 |
0.45 % |
88991 |
0.20 % |
| mq40 |
562799 |
0.11 % |
399442 |
0.09 % |
163357 |
0.36 % |
| qd2,mq40 |
21638 |
0.00 % |
16449 |
0.00 % |
5189 |
0.01 % |
| fs60 |
951 |
0.00 % |
0 |
0.00 % |
951 |
0.00 % |
| q20,qd2,fs60 |
770 |
0.00 % |
0 |
0.00 % |
770 |
0.00 % |
| qd2,fs60 |
265 |
0.00 % |
0 |
0.00 % |
265 |
0.00 % |
| fs60,mq40 |
110 |
0.00 % |
0 |
0.00 % |
110 |
0.00 % |
| qd2,fs60,mq40 |
89 |
0.00 % |
0 |
0.00 % |
89 |
0.00 % |
| q20,qd2,fs60,mq40 |
26 |
0.00 % |
0 |
0.00 % |
26 |
0.00 % |
| q20,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
Coverage and Quality
| Coverage Variants |
Quality Variants |
 |
 |
Filtering Criteria Distribution
| Phred scale strand bias estimated using Fisher's Exact Test. |
 |
| Allele-specific call confidence normalized by depth of sample reads supporting the allele. Variants. |
Allele-specific call confidence normalized by depth of sample reads supporting the allele. Non-Variants. |
 |
 |
| Root Mean Square of the mapping quality of reads. Variants. |
Root Mean Square of the mapping quality of reads. Non-Variants. |
 |
 |
Mutations
| Type |
Mutation |
Status |
# |
% |
| Transition |
A>G |
All |
23948662 |
33.47 % |
| Transition |
G>A |
All |
5000463 |
6.99 % |
| Transition |
T>C |
All |
25471945 |
35.60 % |
| Transition |
C>T |
All |
3406007 |
4.76 % |
| Transversion |
A>C |
All |
1395631 |
1.95 % |
| Transversion |
C>A |
All |
2533821 |
3.54 % |
| Transversion |
T>G |
All |
1566641 |
2.19 % |
| Transversion |
G>T |
All |
2380429 |
3.33 % |
| Transversion |
A>T |
All |
1787857 |
2.50 % |
| Transversion |
T>A |
All |
2035553 |
2.84 % |
| Transversion |
C>G |
All |
1019450 |
1.42 % |
| Transversion |
G>C |
All |
1003311 |
1.40 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2713457 |
25.43 % |
| Transition |
G>A |
Passed |
970801 |
9.10 % |
| Transition |
T>C |
Passed |
4387450 |
41.12 % |
| Transition |
C>T |
Passed |
676411 |
6.34 % |
| Transversion |
A>C |
Passed |
228426 |
2.14 % |
| Transversion |
C>A |
Passed |
308602 |
2.89 % |
| Transversion |
T>G |
Passed |
252484 |
2.37 % |
| Transversion |
G>T |
Passed |
256113 |
2.40 % |
| Transversion |
A>T |
Passed |
172486 |
1.62 % |
| Transversion |
T>A |
Passed |
236832 |
2.22 % |
| Transversion |
C>G |
Passed |
233344 |
2.19 % |
| Transversion |
G>C |
Passed |
234720 |
2.20 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPAll |
0 |
0.00 % |
| Transition |
G>A |
dbSNPAll |
0 |
0.00 % |
| Transition |
T>C |
dbSNPAll |
0 |
0.00 % |
| Transition |
C>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPAll |
0 |
0.00 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPPassed |
0 |
0.00 % |
| Transition |
G>A |
dbSNPPassed |
0 |
0.00 % |
| Transition |
T>C |
dbSNPPassed |
0 |
0.00 % |
| Transition |
C>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPPassed |
0 |
0.00 % |
| |
|
|
|
|
Ti/Tv Ratio
| Status |
Ratio |
Transitions |
Transversions |
| All |
4.21 |
57827077 |
13722693 |
| Passed |
4.55 |
8748119 |
1923007 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |