/EXTERNAL BLUEPRINT/variants/K010413_K010414_K010415_K010416_K010417_K010418_6_lane_gembs
BACK
SAMPLE K010413_K010414_K010415_K010416_K010417_K010418_6_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
844714009 |
2457774 |
0.29 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
844714009 |
100% |
829727129 |
98.23 % |
14986880 |
1.77 % |
| |
|
|
|
|
|
|
| Passed |
9217153 |
1.09 % |
2158840 |
0.26 % |
7058313 |
76.58 % |
| Filtered |
835496856 |
98.91 % |
827568289 |
99.74 % |
7928567 |
86.02 % |
| |
|
|
|
|
|
|
| q20 |
597668042 |
71.53 % |
591831934 |
71.51 % |
5836108 |
73.61 % |
| q20,qd2 |
153133193 |
18.33 % |
151985261 |
18.37 % |
1147932 |
14.48 % |
| q20,mq40 |
56754383 |
6.79 % |
56332238 |
6.81 % |
422145 |
5.32 % |
| q20,qd2,mq40 |
27424464 |
3.28 % |
27340348 |
3.30 % |
84116 |
1.06 % |
| mq40 |
509040 |
0.06 % |
71292 |
0.01 % |
437748 |
5.52 % |
| qd2 |
5836 |
0.00 % |
5707 |
0.00 % |
129 |
0.00 % |
| qd2,mq40 |
1841 |
0.00 % |
1509 |
0.00 % |
332 |
0.00 % |
| fs60,mq40 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| qd2,fs60 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| qd2,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
4443000 |
22.42 % |
| Transition |
G>A |
All |
1565163 |
7.90 % |
| Transition |
T>C |
All |
5442061 |
27.46 % |
| Transition |
C>T |
All |
737840 |
3.72 % |
| Transversion |
A>C |
All |
700266 |
3.53 % |
| Transversion |
C>A |
All |
1283131 |
6.47 % |
| Transversion |
T>G |
All |
862334 |
4.35 % |
| Transversion |
G>T |
All |
1137570 |
5.74 % |
| Transversion |
A>T |
All |
934558 |
4.72 % |
| Transversion |
T>A |
All |
1273530 |
6.43 % |
| Transversion |
C>G |
All |
678561 |
3.42 % |
| Transversion |
G>C |
All |
762546 |
3.85 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
51234 |
17.31 % |
| Transition |
G>A |
Passed |
40432 |
13.66 % |
| Transition |
T>C |
Passed |
80234 |
27.11 % |
| Transition |
C>T |
Passed |
16412 |
5.55 % |
| Transversion |
A>C |
Passed |
12300 |
4.16 % |
| Transversion |
C>A |
Passed |
17782 |
6.01 % |
| Transversion |
T>G |
Passed |
13432 |
4.54 % |
| Transversion |
G>T |
Passed |
9548 |
3.23 % |
| Transversion |
A>T |
Passed |
6036 |
2.04 % |
| Transversion |
T>A |
Passed |
16806 |
5.68 % |
| Transversion |
C>G |
Passed |
13487 |
4.56 % |
| Transversion |
G>C |
Passed |
18269 |
6.17 % |
| |
|
|
|
|
| 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 |
1.60 |
12188064 |
7632496 |
| Passed |
1.75 |
188312 |
107660 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |