/EXTERNAL BLUEPRINT/variants/K006332_15_lane_gembs
BACK
SAMPLE K006332_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1118515734 |
673010815 |
60.17 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1118515734 |
100% |
1099882306 |
98.33 % |
18633428 |
1.67 % |
| |
|
|
|
|
|
|
| Passed |
674861560 |
60.34 % |
671568952 |
61.06 % |
3292608 |
0.49 % |
| Filtered |
443654174 |
39.66 % |
428313354 |
38.94 % |
15340820 |
2.27 % |
| |
|
|
|
|
|
|
| q20 |
370481732 |
83.51 % |
368559037 |
86.05 % |
1922695 |
12.53 % |
| q20,qd2 |
46077124 |
10.39 % |
33306162 |
7.78 % |
12770962 |
83.25 % |
| q20,mq40 |
14505583 |
3.27 % |
14387997 |
3.36 % |
117586 |
0.77 % |
| mq40 |
7007436 |
1.58 % |
6824958 |
1.59 % |
182478 |
1.19 % |
| q20,qd2,mq40 |
3215265 |
0.72 % |
2992953 |
0.70 % |
222312 |
1.45 % |
| qd2 |
2272076 |
0.51 % |
2166444 |
0.51 % |
105632 |
0.69 % |
| qd2,mq40 |
87334 |
0.02 % |
75803 |
0.02 % |
11531 |
0.08 % |
| q20,qd2,fs60 |
2481 |
0.00 % |
0 |
0.00 % |
2481 |
0.02 % |
| fs60 |
1666 |
0.00 % |
0 |
0.00 % |
1666 |
0.01 % |
| qd2,fs60,mq40 |
1366 |
0.00 % |
0 |
0.00 % |
1366 |
0.01 % |
| qd2,fs60 |
1100 |
0.00 % |
0 |
0.00 % |
1100 |
0.01 % |
| fs60,mq40 |
514 |
0.00 % |
0 |
0.00 % |
514 |
0.00 % |
| q20,qd2,fs60,mq40 |
492 |
0.00 % |
0 |
0.00 % |
492 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3657342 |
16.22 % |
| Transition |
G>A |
All |
6386456 |
28.32 % |
| Transition |
T>C |
All |
3275425 |
14.52 % |
| Transition |
C>T |
All |
6190358 |
27.45 % |
| Transversion |
A>C |
All |
229958 |
1.02 % |
| Transversion |
C>A |
All |
609812 |
2.70 % |
| Transversion |
T>G |
All |
260042 |
1.15 % |
| Transversion |
G>T |
All |
594380 |
2.64 % |
| Transversion |
A>T |
All |
465620 |
2.06 % |
| Transversion |
T>A |
All |
473998 |
2.10 % |
| Transversion |
C>G |
All |
209927 |
0.93 % |
| Transversion |
G>C |
All |
197362 |
0.88 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
400246 |
18.95 % |
| Transition |
G>A |
Passed |
357267 |
16.91 % |
| Transition |
T>C |
Passed |
398300 |
18.86 % |
| Transition |
C>T |
Passed |
357638 |
16.93 % |
| Transversion |
A>C |
Passed |
79655 |
3.77 % |
| Transversion |
C>A |
Passed |
73808 |
3.49 % |
| Transversion |
T>G |
Passed |
79312 |
3.75 % |
| Transversion |
G>T |
Passed |
73866 |
3.50 % |
| Transversion |
A>T |
Passed |
51644 |
2.44 % |
| Transversion |
T>A |
Passed |
51058 |
2.42 % |
| Transversion |
C>G |
Passed |
94593 |
4.48 % |
| Transversion |
G>C |
Passed |
94909 |
4.49 % |
| |
|
|
|
|
| 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 |
6.42 |
19509581 |
3041099 |
| Passed |
2.53 |
1513451 |
598845 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |