/EXTERNAL Roadmap/variants/K012798_1_lane_gembs
BACK
SAMPLE K012798_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1135908836 |
66920193 |
5.89 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1135908836 |
100% |
1112753690 |
97.96 % |
23155146 |
2.04 % |
| |
|
|
|
|
|
|
| Passed |
76614959 |
6.74 % |
65834127 |
5.92 % |
10780832 |
14.07 % |
| Filtered |
1059293877 |
93.26 % |
1046919563 |
94.08 % |
12374314 |
16.15 % |
| |
|
|
|
|
|
|
| q20 |
995290651 |
93.96 % |
989253832 |
94.49 % |
6036819 |
48.79 % |
| q20,qd2 |
39376337 |
3.72 % |
33365283 |
3.19 % |
6011054 |
48.58 % |
| q20,mq40 |
17929807 |
1.69 % |
17833659 |
1.70 % |
96148 |
0.78 % |
| q20,qd2,mq40 |
6364494 |
0.60 % |
6296731 |
0.60 % |
67763 |
0.55 % |
| mq40 |
299081 |
0.03 % |
141770 |
0.01 % |
157311 |
1.27 % |
| qd2 |
20572 |
0.00 % |
18128 |
0.00 % |
2444 |
0.02 % |
| qd2,mq40 |
12724 |
0.00 % |
10160 |
0.00 % |
2564 |
0.02 % |
| qd2,fs60,mq40 |
92 |
0.00 % |
0 |
0.00 % |
92 |
0.00 % |
| fs60,mq40 |
57 |
0.00 % |
0 |
0.00 % |
57 |
0.00 % |
| qd2,fs60 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,qd2,fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
8483165 |
33.24 % |
| Transition |
G>A |
All |
1366963 |
5.36 % |
| Transition |
T>C |
All |
5171408 |
20.26 % |
| Transition |
C>T |
All |
1473976 |
5.78 % |
| Transversion |
A>C |
All |
490141 |
1.92 % |
| Transversion |
C>A |
All |
1694647 |
6.64 % |
| Transversion |
T>G |
All |
989758 |
3.88 % |
| Transversion |
G>T |
All |
1460211 |
5.72 % |
| Transversion |
A>T |
All |
1435960 |
5.63 % |
| Transversion |
T>A |
All |
1831364 |
7.18 % |
| Transversion |
C>G |
All |
707208 |
2.77 % |
| Transversion |
G>C |
All |
415751 |
1.63 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
182623 |
15.95 % |
| Transition |
G>A |
Passed |
144182 |
12.59 % |
| Transition |
T>C |
Passed |
158552 |
13.85 % |
| Transition |
C>T |
Passed |
151512 |
13.23 % |
| Transversion |
A>C |
Passed |
62826 |
5.49 % |
| Transversion |
C>A |
Passed |
65790 |
5.74 % |
| Transversion |
T>G |
Passed |
65683 |
5.74 % |
| Transversion |
G>T |
Passed |
66605 |
5.82 % |
| Transversion |
A>T |
Passed |
59571 |
5.20 % |
| Transversion |
T>A |
Passed |
59323 |
5.18 % |
| Transversion |
C>G |
Passed |
65027 |
5.68 % |
| Transversion |
G>C |
Passed |
63491 |
5.54 % |
| |
|
|
|
|
| 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 |
1.83 |
16495512 |
9025040 |
| Passed |
1.25 |
636869 |
508316 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |