/EXTERNAL BLUEPRINT/variants/K006363_14_lane_gembs
BACK
SAMPLE K006363_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1137596662 |
705401302 |
62.01 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1137596662 |
100% |
1125371573 |
98.93 % |
12225089 |
1.07 % |
| |
|
|
|
|
|
|
| Passed |
707465930 |
62.19 % |
703790542 |
62.54 % |
3675388 |
0.52 % |
| Filtered |
430130732 |
37.81 % |
421581031 |
37.46 % |
8549701 |
1.21 % |
| |
|
|
|
|
|
|
| q20 |
375369387 |
87.27 % |
373547400 |
88.61 % |
1821987 |
21.31 % |
| q20,qd2 |
28066832 |
6.53 % |
21913280 |
5.20 % |
6153552 |
71.97 % |
| q20,mq40 |
13820394 |
3.21 % |
13712210 |
3.25 % |
108184 |
1.27 % |
| mq40 |
5556044 |
1.29 % |
5390473 |
1.28 % |
165571 |
1.94 % |
| qd2 |
4126820 |
0.96 % |
4040530 |
0.96 % |
86290 |
1.01 % |
| q20,qd2,mq40 |
3114866 |
0.72 % |
2914187 |
0.69 % |
200679 |
2.35 % |
| qd2,mq40 |
72421 |
0.02 % |
62951 |
0.01 % |
9470 |
0.11 % |
| q20,qd2,fs60 |
962 |
0.00 % |
0 |
0.00 % |
962 |
0.01 % |
| qd2,fs60,mq40 |
934 |
0.00 % |
0 |
0.00 % |
934 |
0.01 % |
| fs60 |
757 |
0.00 % |
0 |
0.00 % |
757 |
0.01 % |
| qd2,fs60 |
568 |
0.00 % |
0 |
0.00 % |
568 |
0.01 % |
| q20,qd2,fs60,mq40 |
376 |
0.00 % |
0 |
0.00 % |
376 |
0.00 % |
| fs60,mq40 |
369 |
0.00 % |
0 |
0.00 % |
369 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3774406 |
26.87 % |
| Transition |
G>A |
All |
1593263 |
11.34 % |
| Transition |
T>C |
All |
3344948 |
23.81 % |
| Transition |
C>T |
All |
1539308 |
10.96 % |
| Transversion |
A>C |
All |
237294 |
1.69 % |
| Transversion |
C>A |
All |
859923 |
6.12 % |
| Transversion |
T>G |
All |
271222 |
1.93 % |
| Transversion |
G>T |
All |
845689 |
6.02 % |
| Transversion |
A>T |
All |
573387 |
4.08 % |
| Transversion |
T>A |
All |
579627 |
4.13 % |
| Transversion |
C>G |
All |
221226 |
1.57 % |
| Transversion |
G>C |
All |
206249 |
1.47 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
422180 |
18.14 % |
| Transition |
G>A |
Passed |
392606 |
16.87 % |
| Transition |
T>C |
Passed |
418949 |
18.01 % |
| Transition |
C>T |
Passed |
393260 |
16.90 % |
| Transversion |
A>C |
Passed |
91690 |
3.94 % |
| Transversion |
C>A |
Passed |
88659 |
3.81 % |
| Transversion |
T>G |
Passed |
91258 |
3.92 % |
| Transversion |
G>T |
Passed |
88592 |
3.81 % |
| Transversion |
A>T |
Passed |
63850 |
2.74 % |
| Transversion |
T>A |
Passed |
63811 |
2.74 % |
| Transversion |
C>G |
Passed |
105694 |
4.54 % |
| Transversion |
G>C |
Passed |
106254 |
4.57 % |
| |
|
|
|
|
| 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 |
2.70 |
10251925 |
3794617 |
| Passed |
2.32 |
1626995 |
699808 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |