/EXTERNAL BLUEPRINT/variants/K011855_K011860_K011861_K011862_K011863_K011864_K011917_K011918_8_lane_gembs
BACK
SAMPLE K011855_K011860_K011861_K011862_K011863_K011864_K011917_K011918_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
633669491 |
605837 |
0.10 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
633669491 |
100% |
628270198 |
99.15 % |
5399293 |
0.85 % |
| |
|
|
|
|
|
|
| Passed |
3736396 |
0.59 % |
535035 |
0.09 % |
3201361 |
85.68 % |
| Filtered |
629933095 |
99.41 % |
627735163 |
99.91 % |
2197932 |
58.82 % |
| |
|
|
|
|
|
|
| q20 |
513393959 |
81.50 % |
511712084 |
81.52 % |
1681875 |
76.52 % |
| q20,qd2 |
66249260 |
10.52 % |
66001460 |
10.51 % |
247800 |
11.27 % |
| q20,mq40 |
39802137 |
6.32 % |
39698084 |
6.32 % |
104053 |
4.73 % |
| q20,qd2,mq40 |
10304216 |
1.64 % |
10287439 |
1.64 % |
16777 |
0.76 % |
| mq40 |
181009 |
0.03 % |
33830 |
0.01 % |
147179 |
6.70 % |
| qd2 |
1812 |
0.00 % |
1704 |
0.00 % |
108 |
0.00 % |
| qd2,mq40 |
685 |
0.00 % |
562 |
0.00 % |
123 |
0.01 % |
| fs60,mq40 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| 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 % |
| q20,qd2,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 |
2096519 |
21.83 % |
| Transition |
G>A |
All |
750709 |
7.82 % |
| Transition |
T>C |
All |
2710598 |
28.23 % |
| Transition |
C>T |
All |
400706 |
4.17 % |
| Transversion |
A>C |
All |
392602 |
4.09 % |
| Transversion |
C>A |
All |
544551 |
5.67 % |
| Transversion |
T>G |
All |
402768 |
4.19 % |
| Transversion |
G>T |
All |
508189 |
5.29 % |
| Transversion |
A>T |
All |
458212 |
4.77 % |
| Transversion |
T>A |
All |
618291 |
6.44 % |
| Transversion |
C>G |
All |
330290 |
3.44 % |
| Transversion |
G>C |
All |
389413 |
4.06 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
10699 |
15.21 % |
| Transition |
G>A |
Passed |
9076 |
12.90 % |
| Transition |
T>C |
Passed |
15727 |
22.36 % |
| Transition |
C>T |
Passed |
5102 |
7.25 % |
| Transversion |
A>C |
Passed |
3727 |
5.30 % |
| Transversion |
C>A |
Passed |
3852 |
5.48 % |
| Transversion |
T>G |
Passed |
3564 |
5.07 % |
| Transversion |
G>T |
Passed |
3033 |
4.31 % |
| Transversion |
A>T |
Passed |
2331 |
3.31 % |
| Transversion |
T>A |
Passed |
3895 |
5.54 % |
| Transversion |
C>G |
Passed |
4229 |
6.01 % |
| Transversion |
G>C |
Passed |
5108 |
7.26 % |
| |
|
|
|
|
| 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 |
1.64 |
5958532 |
3644316 |
| Passed |
1.37 |
40604 |
29739 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |