/EXTERNAL KNIH/variants/K006252_1_lane_gembs
BACK
SAMPLE K006252_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1137773090 |
441109235 |
38.77 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1137773090 |
100% |
1082864859 |
95.17 % |
54908231 |
4.83 % |
| |
|
|
|
|
|
|
| Passed |
452339536 |
39.76 % |
434094162 |
40.09 % |
18245374 |
4.03 % |
| Filtered |
685433554 |
60.24 % |
648770697 |
59.91 % |
36662857 |
8.11 % |
| |
|
|
|
|
|
|
| q20 |
599872758 |
87.52 % |
585097300 |
90.19 % |
14775458 |
40.30 % |
| q20,qd2 |
72695540 |
10.61 % |
51808643 |
7.99 % |
20886897 |
56.97 % |
| q20,mq40 |
5056306 |
0.74 % |
4939995 |
0.76 % |
116311 |
0.32 % |
| qd2 |
4713642 |
0.69 % |
4022851 |
0.62 % |
690791 |
1.88 % |
| q20,qd2,mq40 |
2659449 |
0.39 % |
2588141 |
0.40 % |
71308 |
0.19 % |
| mq40 |
415788 |
0.06 % |
298949 |
0.05 % |
116839 |
0.32 % |
| qd2,mq40 |
19032 |
0.00 % |
14818 |
0.00 % |
4214 |
0.01 % |
| fs60 |
399 |
0.00 % |
0 |
0.00 % |
399 |
0.00 % |
| q20,qd2,fs60 |
386 |
0.00 % |
0 |
0.00 % |
386 |
0.00 % |
| qd2,fs60 |
145 |
0.00 % |
0 |
0.00 % |
145 |
0.00 % |
| fs60,mq40 |
45 |
0.00 % |
0 |
0.00 % |
45 |
0.00 % |
| qd2,fs60,mq40 |
45 |
0.00 % |
0 |
0.00 % |
45 |
0.00 % |
| q20,qd2,fs60,mq40 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
17432036 |
30.27 % |
| Transition |
G>A |
All |
3684370 |
6.40 % |
| Transition |
T>C |
All |
17185086 |
29.84 % |
| Transition |
C>T |
All |
2550495 |
4.43 % |
| Transversion |
A>C |
All |
1445471 |
2.51 % |
| Transversion |
C>A |
All |
3269179 |
5.68 % |
| Transversion |
T>G |
All |
1653157 |
2.87 % |
| Transversion |
G>T |
All |
3045185 |
5.29 % |
| Transversion |
A>T |
All |
2331851 |
4.05 % |
| Transversion |
T>A |
All |
2624903 |
4.56 % |
| Transversion |
C>G |
All |
1180375 |
2.05 % |
| Transversion |
G>C |
All |
1185789 |
2.06 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2025095 |
27.31 % |
| Transition |
G>A |
Passed |
751582 |
10.13 % |
| Transition |
T>C |
Passed |
2712141 |
36.57 % |
| Transition |
C>T |
Passed |
479465 |
6.46 % |
| Transversion |
A>C |
Passed |
183626 |
2.48 % |
| Transversion |
C>A |
Passed |
210558 |
2.84 % |
| Transversion |
T>G |
Passed |
207982 |
2.80 % |
| Transversion |
G>T |
Passed |
148565 |
2.00 % |
| Transversion |
A>T |
Passed |
107468 |
1.45 % |
| Transversion |
T>A |
Passed |
167494 |
2.26 % |
| Transversion |
C>G |
Passed |
204309 |
2.75 % |
| Transversion |
G>C |
Passed |
218163 |
2.94 % |
| |
|
|
|
|
| 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 |
2.44 |
40851987 |
16735910 |
| Passed |
4.12 |
5968283 |
1448165 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |