/EXTERNAL KNIH/variants/K006232_1_lane_gembs
BACK
SAMPLE K006232_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1161743635 |
1042256953 |
89.71 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1161743635 |
100% |
1147142780 |
98.74 % |
14600855 |
1.26 % |
| |
|
|
|
|
|
|
| Passed |
1043684580 |
89.84 % |
1039744101 |
90.64 % |
3940479 |
0.38 % |
| Filtered |
118059055 |
10.16 % |
107398679 |
9.36 % |
10660376 |
1.02 % |
| |
|
|
|
|
|
|
| q20 |
78516437 |
66.51 % |
77475169 |
72.14 % |
1041268 |
9.77 % |
| q20,mq40 |
14978290 |
12.69 % |
14820535 |
13.80 % |
157755 |
1.48 % |
| q20,qd2 |
11230130 |
9.51 % |
2775996 |
2.58 % |
8454134 |
79.30 % |
| mq40 |
7968546 |
6.75 % |
7649547 |
7.12 % |
318999 |
2.99 % |
| q20,qd2,mq40 |
3062111 |
2.59 % |
2792000 |
2.60 % |
270111 |
2.53 % |
| qd2 |
2214661 |
1.88 % |
1814212 |
1.69 % |
400449 |
3.76 % |
| qd2,mq40 |
85392 |
0.07 % |
71220 |
0.07 % |
14172 |
0.13 % |
| qd2,fs60,mq40 |
1426 |
0.00 % |
0 |
0.00 % |
1426 |
0.01 % |
| fs60,mq40 |
576 |
0.00 % |
0 |
0.00 % |
576 |
0.01 % |
| fs60 |
564 |
0.00 % |
0 |
0.00 % |
564 |
0.01 % |
| qd2,fs60 |
493 |
0.00 % |
0 |
0.00 % |
493 |
0.00 % |
| q20,qd2,fs60 |
268 |
0.00 % |
0 |
0.00 % |
268 |
0.00 % |
| q20,qd2,fs60,mq40 |
156 |
0.00 % |
0 |
0.00 % |
156 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60 |
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 |
6206511 |
37.77 % |
| Transition |
G>A |
All |
881276 |
5.36 % |
| Transition |
T>C |
All |
6168650 |
37.54 % |
| Transition |
C>T |
All |
885394 |
5.39 % |
| Transversion |
A>C |
All |
237150 |
1.44 % |
| Transversion |
C>A |
All |
380106 |
2.31 % |
| Transversion |
T>G |
All |
239961 |
1.46 % |
| Transversion |
G>T |
All |
374171 |
2.28 % |
| Transversion |
A>T |
All |
317560 |
1.93 % |
| Transversion |
T>A |
All |
309527 |
1.88 % |
| Transversion |
C>G |
All |
215929 |
1.31 % |
| Transversion |
G>C |
All |
216099 |
1.32 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
740369 |
19.41 % |
| Transition |
G>A |
Passed |
581016 |
15.23 % |
| Transition |
T>C |
Passed |
742038 |
19.45 % |
| Transition |
C>T |
Passed |
583877 |
15.31 % |
| Transversion |
A>C |
Passed |
150070 |
3.93 % |
| Transversion |
C>A |
Passed |
152076 |
3.99 % |
| Transversion |
T>G |
Passed |
150956 |
3.96 % |
| Transversion |
G>T |
Passed |
151465 |
3.97 % |
| Transversion |
A>T |
Passed |
131594 |
3.45 % |
| Transversion |
T>A |
Passed |
131509 |
3.45 % |
| Transversion |
C>G |
Passed |
149646 |
3.92 % |
| Transversion |
G>C |
Passed |
150177 |
3.94 % |
| |
|
|
|
|
| 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 |
6.17 |
14141831 |
2290503 |
| Passed |
2.27 |
2647300 |
1167493 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |