/EXTERNAL BLUEPRINT/variants/K010527_1_lane_gembs
BACK
SAMPLE K010527_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1121455827 |
233221638 |
20.80 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1121455827 |
100% |
1095435650 |
97.68 % |
26020177 |
2.32 % |
| |
|
|
|
|
|
|
| Passed |
241439949 |
21.53 % |
232109671 |
21.19 % |
9330278 |
3.86 % |
| Filtered |
880015878 |
78.47 % |
863325979 |
78.81 % |
16689899 |
6.91 % |
| |
|
|
|
|
|
|
| q20 |
804468204 |
91.42 % |
798147521 |
92.45 % |
6320683 |
37.87 % |
| q20,qd2 |
57582022 |
6.54 % |
47482549 |
5.50 % |
10099473 |
60.51 % |
| q20,mq40 |
12282916 |
1.40 % |
12198642 |
1.41 % |
84274 |
0.50 % |
| q20,qd2,mq40 |
5234694 |
0.59 % |
5173205 |
0.60 % |
61489 |
0.37 % |
| mq40 |
338428 |
0.04 % |
227387 |
0.03 % |
111041 |
0.67 % |
| qd2 |
93763 |
0.01 % |
83840 |
0.01 % |
9923 |
0.06 % |
| qd2,mq40 |
15496 |
0.00 % |
12835 |
0.00 % |
2661 |
0.02 % |
| qd2,fs60,mq40 |
170 |
0.00 % |
0 |
0.00 % |
170 |
0.00 % |
| fs60,mq40 |
76 |
0.00 % |
0 |
0.00 % |
76 |
0.00 % |
| qd2,fs60 |
54 |
0.00 % |
0 |
0.00 % |
54 |
0.00 % |
| q20,qd2,fs60,mq40 |
31 |
0.00 % |
0 |
0.00 % |
31 |
0.00 % |
| fs60 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| q20,qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
8840180 |
31.49 % |
| Transition |
G>A |
All |
1264903 |
4.51 % |
| Transition |
T>C |
All |
8892581 |
31.68 % |
| Transition |
C>T |
All |
1267808 |
4.52 % |
| Transversion |
A>C |
All |
429903 |
1.53 % |
| Transversion |
C>A |
All |
1393439 |
4.96 % |
| Transversion |
T>G |
All |
427734 |
1.52 % |
| Transversion |
G>T |
All |
1380672 |
4.92 % |
| Transversion |
A>T |
All |
1767261 |
6.30 % |
| Transversion |
T>A |
All |
1779203 |
6.34 % |
| Transversion |
C>G |
All |
312825 |
1.11 % |
| Transversion |
G>C |
All |
314926 |
1.12 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
257201 |
18.91 % |
| Transition |
G>A |
Passed |
194557 |
14.30 % |
| Transition |
T>C |
Passed |
254882 |
18.74 % |
| Transition |
C>T |
Passed |
195534 |
14.38 % |
| Transversion |
A>C |
Passed |
56607 |
4.16 % |
| Transversion |
C>A |
Passed |
61268 |
4.50 % |
| Transversion |
T>G |
Passed |
57167 |
4.20 % |
| Transversion |
G>T |
Passed |
60703 |
4.46 % |
| Transversion |
A>T |
Passed |
57048 |
4.19 % |
| Transversion |
T>A |
Passed |
57577 |
4.23 % |
| Transversion |
C>G |
Passed |
53969 |
3.97 % |
| Transversion |
G>C |
Passed |
53688 |
3.95 % |
| |
|
|
|
|
| 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 |
2.60 |
20265472 |
7805963 |
| Passed |
1.97 |
902174 |
458027 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |