/EXTERNAL Roadmap/variants/K012806_1_lane_gembs
BACK
SAMPLE K012806_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1124351793 |
33058719 |
2.94 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1124351793 |
100% |
1099995995 |
97.83 % |
24355798 |
2.17 % |
| |
|
|
|
|
|
|
| Passed |
42476340 |
3.78 % |
32412297 |
2.95 % |
10064043 |
23.69 % |
| Filtered |
1081875453 |
96.22 % |
1067583698 |
97.05 % |
14291755 |
33.65 % |
| |
|
|
|
|
|
|
| q20 |
993762722 |
91.86 % |
986753769 |
92.43 % |
7008953 |
49.04 % |
| q20,qd2 |
59879608 |
5.53 % |
52949578 |
4.96 % |
6930030 |
48.49 % |
| q20,mq40 |
19473541 |
1.80 % |
19348147 |
1.81 % |
125394 |
0.88 % |
| q20,qd2,mq40 |
8497530 |
0.79 % |
8417271 |
0.79 % |
80259 |
0.56 % |
| mq40 |
238408 |
0.02 % |
94484 |
0.01 % |
143924 |
1.01 % |
| qd2 |
14298 |
0.00 % |
13016 |
0.00 % |
1282 |
0.01 % |
| qd2,mq40 |
9226 |
0.00 % |
7433 |
0.00 % |
1793 |
0.01 % |
| qd2,fs60,mq40 |
54 |
0.00 % |
0 |
0.00 % |
54 |
0.00 % |
| fs60,mq40 |
34 |
0.00 % |
0 |
0.00 % |
34 |
0.00 % |
| qd2,fs60 |
25 |
0.00 % |
0 |
0.00 % |
25 |
0.00 % |
| q20,qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
7690222 |
28.68 % |
| Transition |
G>A |
All |
1479658 |
5.52 % |
| Transition |
T>C |
All |
4434644 |
16.54 % |
| Transition |
C>T |
All |
1569267 |
5.85 % |
| Transversion |
A>C |
All |
554693 |
2.07 % |
| Transversion |
C>A |
All |
2218566 |
8.27 % |
| Transversion |
T>G |
All |
1038903 |
3.87 % |
| Transversion |
G>T |
All |
2000575 |
7.46 % |
| Transversion |
A>T |
All |
2157771 |
8.05 % |
| Transversion |
T>A |
All |
2513734 |
9.38 % |
| Transversion |
C>G |
All |
717381 |
2.68 % |
| Transversion |
G>C |
All |
435395 |
1.62 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
105789 |
15.83 % |
| Transition |
G>A |
Passed |
77809 |
11.65 % |
| Transition |
T>C |
Passed |
84675 |
12.67 % |
| Transition |
C>T |
Passed |
82149 |
12.30 % |
| Transversion |
A>C |
Passed |
38250 |
5.73 % |
| Transversion |
C>A |
Passed |
41542 |
6.22 % |
| Transversion |
T>G |
Passed |
41304 |
6.18 % |
| Transversion |
G>T |
Passed |
41409 |
6.20 % |
| Transversion |
A>T |
Passed |
39346 |
5.89 % |
| Transversion |
T>A |
Passed |
39443 |
5.90 % |
| Transversion |
C>G |
Passed |
39190 |
5.87 % |
| Transversion |
G>C |
Passed |
37192 |
5.57 % |
| |
|
|
|
|
| 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 |
1.30 |
15173791 |
11637018 |
| Passed |
1.10 |
350422 |
317676 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |