/EXTERNAL BLUEPRINT/variants/K012039_K012080_K012081_K012082_K012083_K012084_K012085_K012086_K012087_K012118_K012119_11_lane_gembs
BACK
SAMPLE K012039_K012080_K012081_K012082_K012083_K012084_K012085_K012086_K012087_K012118_K012119_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
844612916 |
3522170 |
0.42 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
844612916 |
100% |
831708547 |
98.47 % |
12904369 |
1.53 % |
| |
|
|
|
|
|
|
| Passed |
10891183 |
1.29 % |
3194415 |
0.38 % |
7696768 |
70.67 % |
| Filtered |
833721733 |
98.71 % |
828514132 |
99.62 % |
5207601 |
47.81 % |
| |
|
|
|
|
|
|
| q20 |
667812064 |
80.10 % |
664087401 |
80.15 % |
3724663 |
71.52 % |
| q20,qd2 |
102059871 |
12.24 % |
101199422 |
12.21 % |
860449 |
16.52 % |
| q20,mq40 |
47757153 |
5.73 % |
47532800 |
5.74 % |
224353 |
4.31 % |
| q20,qd2,mq40 |
15652886 |
1.88 % |
15602934 |
1.88 % |
49952 |
0.96 % |
| mq40 |
433052 |
0.05 % |
85495 |
0.01 % |
347557 |
6.67 % |
| qd2 |
5189 |
0.00 % |
4908 |
0.00 % |
281 |
0.01 % |
| qd2,mq40 |
1472 |
0.00 % |
1172 |
0.00 % |
300 |
0.01 % |
| fs60,mq40 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| qd2,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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,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 |
3902584 |
22.52 % |
| Transition |
G>A |
All |
1387620 |
8.01 % |
| Transition |
T>C |
All |
4938471 |
28.50 % |
| Transition |
C>T |
All |
674328 |
3.89 % |
| Transversion |
A>C |
All |
601532 |
3.47 % |
| Transversion |
C>A |
All |
1064271 |
6.14 % |
| Transversion |
T>G |
All |
699432 |
4.04 % |
| Transversion |
G>T |
All |
959668 |
5.54 % |
| Transversion |
A>T |
All |
792358 |
4.57 % |
| Transversion |
T>A |
All |
1115832 |
6.44 % |
| Transversion |
C>G |
All |
549455 |
3.17 % |
| Transversion |
G>C |
All |
642858 |
3.71 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
55473 |
17.04 % |
| Transition |
G>A |
Passed |
42253 |
12.98 % |
| Transition |
T>C |
Passed |
78945 |
24.24 % |
| Transition |
C>T |
Passed |
20838 |
6.40 % |
| Transversion |
A>C |
Passed |
14256 |
4.38 % |
| Transversion |
C>A |
Passed |
19790 |
6.08 % |
| Transversion |
T>G |
Passed |
16066 |
4.93 % |
| Transversion |
G>T |
Passed |
13130 |
4.03 % |
| Transversion |
A>T |
Passed |
8774 |
2.69 % |
| Transversion |
T>A |
Passed |
18459 |
5.67 % |
| Transversion |
C>G |
Passed |
17168 |
5.27 % |
| Transversion |
G>C |
Passed |
20468 |
6.29 % |
| |
|
|
|
|
| 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 |
1.70 |
10903003 |
6425406 |
| Passed |
1.54 |
197509 |
128111 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |