/EXTERNAL McGill EMC/variants/K006173_1_lane_gembs
BACK
SAMPLE K006173_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1151456033 |
886586462 |
77.00 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1151456033 |
100% |
1137054796 |
98.75 % |
14401237 |
1.25 % |
| |
|
|
|
|
|
|
| Passed |
888246380 |
77.14 % |
884259989 |
77.77 % |
3986391 |
0.45 % |
| Filtered |
263209653 |
22.86 % |
252794807 |
22.23 % |
10414846 |
1.17 % |
| |
|
|
|
|
|
|
| q20 |
230688687 |
87.64 % |
229319083 |
90.71 % |
1369604 |
13.15 % |
| q20,qd2 |
14015086 |
5.32 % |
5376388 |
2.13 % |
8638698 |
82.95 % |
| q20,mq40 |
12903498 |
4.90 % |
12810732 |
5.07 % |
92766 |
0.89 % |
| q20,qd2,mq40 |
3590176 |
1.36 % |
3495278 |
1.38 % |
94898 |
0.91 % |
| mq40 |
1381480 |
0.52 % |
1220678 |
0.48 % |
160802 |
1.54 % |
| qd2 |
601639 |
0.23 % |
550084 |
0.22 % |
51555 |
0.50 % |
| qd2,mq40 |
28471 |
0.01 % |
22564 |
0.01 % |
5907 |
0.06 % |
| qd2,fs60,mq40 |
368 |
0.00 % |
0 |
0.00 % |
368 |
0.00 % |
| fs60,mq40 |
119 |
0.00 % |
0 |
0.00 % |
119 |
0.00 % |
| qd2,fs60 |
86 |
0.00 % |
0 |
0.00 % |
86 |
0.00 % |
| fs60 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| q20,qd2,fs60,mq40 |
20 |
0.00 % |
0 |
0.00 % |
20 |
0.00 % |
| q20,qd2,fs60 |
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 |
5767867 |
35.98 % |
| Transition |
G>A |
All |
1034184 |
6.45 % |
| Transition |
T>C |
All |
5595824 |
34.90 % |
| Transition |
C>T |
All |
1059796 |
6.61 % |
| Transversion |
A>C |
All |
231487 |
1.44 % |
| Transversion |
C>A |
All |
453471 |
2.83 % |
| Transversion |
T>G |
All |
235181 |
1.47 % |
| Transversion |
G>T |
All |
435809 |
2.72 % |
| Transversion |
A>T |
All |
378586 |
2.36 % |
| Transversion |
T>A |
All |
381237 |
2.38 % |
| Transversion |
C>G |
All |
231159 |
1.44 % |
| Transversion |
G>C |
All |
227572 |
1.42 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
577339 |
17.51 % |
| Transition |
G>A |
Passed |
518020 |
15.71 % |
| Transition |
T>C |
Passed |
581328 |
17.63 % |
| Transition |
C>T |
Passed |
522074 |
15.83 % |
| Transversion |
A>C |
Passed |
138174 |
4.19 % |
| Transversion |
C>A |
Passed |
144308 |
4.38 % |
| Transversion |
T>G |
Passed |
138466 |
4.20 % |
| Transversion |
G>T |
Passed |
144145 |
4.37 % |
| Transversion |
A>T |
Passed |
127162 |
3.86 % |
| Transversion |
T>A |
Passed |
126898 |
3.85 % |
| Transversion |
C>G |
Passed |
139978 |
4.24 % |
| Transversion |
G>C |
Passed |
139739 |
4.24 % |
| |
|
|
|
|
| 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 |
5.23 |
13457671 |
2574502 |
| Passed |
2.00 |
2198761 |
1098870 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |