/EXTERNAL BLUEPRINT/variants/K010461_K010462_K010463_K010464_K010465_K010466_K010467_K010468_K010469_K010470_10_lane_gembs
BACK
SAMPLE K010461_K010462_K010463_K010464_K010465_K010466_K010467_K010468_K010469_K010470_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
907066572 |
6138833 |
0.68 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
907066572 |
100% |
887494032 |
97.84 % |
19572540 |
2.16 % |
| |
|
|
|
|
|
|
| Passed |
14670761 |
1.62 % |
5602983 |
0.63 % |
9067778 |
61.81 % |
| Filtered |
892395811 |
98.38 % |
881891049 |
99.37 % |
10504762 |
71.60 % |
| |
|
|
|
|
|
|
| q20 |
671045922 |
75.20 % |
663531350 |
75.24 % |
7514572 |
71.53 % |
| q20,qd2 |
131416347 |
14.73 % |
129665725 |
14.70 % |
1750622 |
16.67 % |
| q20,mq40 |
63163936 |
7.08 % |
62612297 |
7.10 % |
551639 |
5.25 % |
| q20,qd2,mq40 |
26052283 |
2.92 % |
25934534 |
2.94 % |
117749 |
1.12 % |
| mq40 |
708930 |
0.08 % |
139588 |
0.02 % |
569342 |
5.42 % |
| qd2 |
6078 |
0.00 % |
5730 |
0.00 % |
348 |
0.00 % |
| qd2,mq40 |
2262 |
0.00 % |
1825 |
0.00 % |
437 |
0.00 % |
| fs60,mq40 |
25 |
0.00 % |
0 |
0.00 % |
25 |
0.00 % |
| fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| qd2,fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
5463565 |
22.45 % |
| Transition |
G>A |
All |
1909944 |
7.85 % |
| Transition |
T>C |
All |
6662635 |
27.37 % |
| Transition |
C>T |
All |
881379 |
3.62 % |
| Transversion |
A>C |
All |
898056 |
3.69 % |
| Transversion |
C>A |
All |
1564239 |
6.43 % |
| Transversion |
T>G |
All |
1074142 |
4.41 % |
| Transversion |
G>T |
All |
1401264 |
5.76 % |
| Transversion |
A>T |
All |
1134821 |
4.66 % |
| Transversion |
T>A |
All |
1547229 |
6.36 % |
| Transversion |
C>G |
All |
843987 |
3.47 % |
| Transversion |
G>C |
All |
959918 |
3.94 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
95424 |
17.91 % |
| Transition |
G>A |
Passed |
73006 |
13.70 % |
| Transition |
T>C |
Passed |
145877 |
27.38 % |
| Transition |
C>T |
Passed |
26775 |
5.02 % |
| Transversion |
A>C |
Passed |
21362 |
4.01 % |
| Transversion |
C>A |
Passed |
32726 |
6.14 % |
| Transversion |
T>G |
Passed |
24163 |
4.53 % |
| Transversion |
G>T |
Passed |
16630 |
3.12 % |
| Transversion |
A>T |
Passed |
10688 |
2.01 % |
| Transversion |
T>A |
Passed |
31233 |
5.86 % |
| Transversion |
C>G |
Passed |
22785 |
4.28 % |
| Transversion |
G>C |
Passed |
32206 |
6.04 % |
| |
|
|
|
|
| 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 |
1.58 |
14917523 |
9423656 |
| Passed |
1.78 |
341082 |
191793 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |