/EXTERNAL BLUEPRINT/variants/K006340_12_lane_gembs
BACK
SAMPLE K006340_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1105658120 |
637412008 |
57.65 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1105658120 |
100% |
1088997719 |
98.49 % |
16660401 |
1.51 % |
| |
|
|
|
|
|
|
| Passed |
639021015 |
57.80 % |
636091606 |
58.41 % |
2929409 |
0.46 % |
| Filtered |
466637105 |
42.20 % |
452906113 |
41.59 % |
13730992 |
2.15 % |
| |
|
|
|
|
|
|
| q20 |
391354858 |
83.87 % |
389735905 |
86.05 % |
1618953 |
11.79 % |
| q20,qd2 |
48385671 |
10.37 % |
36841065 |
8.13 % |
11544606 |
84.08 % |
| q20,mq40 |
14688495 |
3.15 % |
14579478 |
3.22 % |
109017 |
0.79 % |
| mq40 |
6636913 |
1.42 % |
6478467 |
1.43 % |
158446 |
1.15 % |
| q20,qd2,mq40 |
3331653 |
0.71 % |
3133274 |
0.69 % |
198379 |
1.44 % |
| qd2 |
2153603 |
0.46 % |
2069422 |
0.46 % |
84181 |
0.61 % |
| qd2,mq40 |
78893 |
0.02 % |
68502 |
0.02 % |
10391 |
0.08 % |
| q20,qd2,fs60 |
2121 |
0.00 % |
0 |
0.00 % |
2121 |
0.02 % |
| fs60 |
1621 |
0.00 % |
0 |
0.00 % |
1621 |
0.01 % |
| qd2,fs60,mq40 |
1282 |
0.00 % |
0 |
0.00 % |
1282 |
0.01 % |
| qd2,fs60 |
897 |
0.00 % |
0 |
0.00 % |
897 |
0.01 % |
| fs60,mq40 |
561 |
0.00 % |
0 |
0.00 % |
561 |
0.00 % |
| q20,qd2,fs60,mq40 |
534 |
0.00 % |
0 |
0.00 % |
534 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3060045 |
15.34 % |
| Transition |
G>A |
All |
5598038 |
28.07 % |
| Transition |
T>C |
All |
2891583 |
14.50 % |
| Transition |
C>T |
All |
5448915 |
27.32 % |
| Transversion |
A>C |
All |
219906 |
1.10 % |
| Transversion |
C>A |
All |
610808 |
3.06 % |
| Transversion |
T>G |
All |
234161 |
1.17 % |
| Transversion |
G>T |
All |
606607 |
3.04 % |
| Transversion |
A>T |
All |
452415 |
2.27 % |
| Transversion |
T>A |
All |
445920 |
2.24 % |
| Transversion |
C>G |
All |
193815 |
0.97 % |
| Transversion |
G>C |
All |
183788 |
0.92 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
366319 |
18.61 % |
| Transition |
G>A |
Passed |
338906 |
17.22 % |
| Transition |
T>C |
Passed |
364852 |
18.54 % |
| Transition |
C>T |
Passed |
340201 |
17.29 % |
| Transversion |
A>C |
Passed |
74949 |
3.81 % |
| Transversion |
C>A |
Passed |
68344 |
3.47 % |
| Transversion |
T>G |
Passed |
74552 |
3.79 % |
| Transversion |
G>T |
Passed |
69018 |
3.51 % |
| Transversion |
A>T |
Passed |
46360 |
2.36 % |
| Transversion |
T>A |
Passed |
46245 |
2.35 % |
| Transversion |
C>G |
Passed |
88676 |
4.51 % |
| Transversion |
G>C |
Passed |
89517 |
4.55 % |
| |
|
|
|
|
| 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 |
5.77 |
16998581 |
2947420 |
| Passed |
2.53 |
1410278 |
557661 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |