/EXTERNAL BLUEPRINT/variants/K011859_K011888_K011889_K011890_K011891_K011892_K011893_K011925_K011926_9_lane_gembs
BACK
SAMPLE K011859_K011888_K011889_K011890_K011891_K011892_K011893_K011925_K011926_9_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
659994722 |
843097 |
0.13 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
659994722 |
100% |
653473410 |
99.01 % |
6521312 |
0.99 % |
| |
|
|
|
|
|
|
| Passed |
4425559 |
0.67 % |
711354 |
0.11 % |
3714205 |
83.93 % |
| Filtered |
655569163 |
99.33 % |
652762056 |
99.89 % |
2807107 |
63.43 % |
| |
|
|
|
|
|
|
| q20 |
504804000 |
77.00 % |
502712402 |
77.01 % |
2091598 |
74.51 % |
| q20,qd2 |
94855463 |
14.47 % |
94498571 |
14.48 % |
356892 |
12.71 % |
| q20,mq40 |
41577662 |
6.34 % |
41435830 |
6.35 % |
141832 |
5.05 % |
| q20,qd2,mq40 |
14098463 |
2.15 % |
14073650 |
2.16 % |
24813 |
0.88 % |
| mq40 |
229189 |
0.03 % |
37451 |
0.01 % |
191738 |
6.83 % |
| qd2 |
3763 |
0.00 % |
3670 |
0.00 % |
93 |
0.00 % |
| qd2,mq40 |
604 |
0.00 % |
482 |
0.00 % |
122 |
0.00 % |
| qd2,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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,qd2,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 |
2427100 |
22.07 % |
| Transition |
G>A |
All |
865640 |
7.87 % |
| Transition |
T>C |
All |
3118735 |
28.36 % |
| Transition |
C>T |
All |
425907 |
3.87 % |
| Transversion |
A>C |
All |
404084 |
3.67 % |
| Transversion |
C>A |
All |
669997 |
6.09 % |
| Transversion |
T>G |
All |
456968 |
4.16 % |
| Transversion |
G>T |
All |
614332 |
5.59 % |
| Transversion |
A>T |
All |
508969 |
4.63 % |
| Transversion |
T>A |
All |
713265 |
6.49 % |
| Transversion |
C>G |
All |
360302 |
3.28 % |
| Transversion |
G>C |
All |
432064 |
3.93 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
21087 |
16.14 % |
| Transition |
G>A |
Passed |
17562 |
13.44 % |
| Transition |
T>C |
Passed |
30054 |
23.00 % |
| Transition |
C>T |
Passed |
7158 |
5.48 % |
| Transversion |
A>C |
Passed |
6174 |
4.72 % |
| Transversion |
C>A |
Passed |
8348 |
6.39 % |
| Transversion |
T>G |
Passed |
6647 |
5.09 % |
| Transversion |
G>T |
Passed |
4893 |
3.74 % |
| Transversion |
A>T |
Passed |
3394 |
2.60 % |
| Transversion |
T>A |
Passed |
8607 |
6.59 % |
| Transversion |
C>G |
Passed |
7140 |
5.46 % |
| Transversion |
G>C |
Passed |
9618 |
7.36 % |
| |
|
|
|
|
| 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 |
6837382 |
4159981 |
| Passed |
1.38 |
75861 |
54821 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |