/EXTERNAL McGill EMC/variants/K006162_1_lane_gembs
BACK
SAMPLE K006162_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1140840194 |
448284118 |
39.29 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1140840194 |
100% |
1128579285 |
98.93 % |
12260909 |
1.07 % |
| |
|
|
|
|
|
|
| Passed |
451004340 |
39.53 % |
446671860 |
39.58 % |
4332480 |
0.96 % |
| Filtered |
689835854 |
60.47 % |
681907425 |
60.42 % |
7928429 |
1.76 % |
| |
|
|
|
|
|
|
| q20 |
654911095 |
94.94 % |
652736895 |
95.72 % |
2174200 |
27.42 % |
| q20,qd2 |
18667300 |
2.71 % |
13217731 |
1.94 % |
5449569 |
68.73 % |
| q20,mq40 |
11351081 |
1.65 % |
11276034 |
1.65 % |
75047 |
0.95 % |
| q20,qd2,mq40 |
3194839 |
0.46 % |
3118525 |
0.46 % |
76314 |
0.96 % |
| qd2 |
917145 |
0.13 % |
890568 |
0.13 % |
26577 |
0.34 % |
| mq40 |
758670 |
0.11 % |
639795 |
0.09 % |
118875 |
1.50 % |
| qd2,mq40 |
34611 |
0.01 % |
27877 |
0.00 % |
6734 |
0.08 % |
| qd2,fs60,mq40 |
572 |
0.00 % |
0 |
0.00 % |
572 |
0.01 % |
| fs60,mq40 |
245 |
0.00 % |
0 |
0.00 % |
245 |
0.00 % |
| qd2,fs60 |
155 |
0.00 % |
0 |
0.00 % |
155 |
0.00 % |
| fs60 |
60 |
0.00 % |
0 |
0.00 % |
60 |
0.00 % |
| q20,qd2,fs60,mq40 |
59 |
0.00 % |
0 |
0.00 % |
59 |
0.00 % |
| q20,qd2,fs60 |
22 |
0.00 % |
0 |
0.00 % |
22 |
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 |
4004738 |
28.58 % |
| Transition |
G>A |
All |
971580 |
6.93 % |
| Transition |
T>C |
All |
3638154 |
25.96 % |
| Transition |
C>T |
All |
998131 |
7.12 % |
| Transversion |
A>C |
All |
318653 |
2.27 % |
| Transversion |
C>A |
All |
1079571 |
7.70 % |
| Transversion |
T>G |
All |
349959 |
2.50 % |
| Transversion |
G>T |
All |
1053156 |
7.51 % |
| Transversion |
A>T |
All |
471510 |
3.36 % |
| Transversion |
T>A |
All |
492940 |
3.52 % |
| Transversion |
C>G |
All |
326958 |
2.33 % |
| Transversion |
G>C |
All |
308707 |
2.20 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
342756 |
16.16 % |
| Transition |
G>A |
Passed |
326272 |
15.39 % |
| Transition |
T>C |
Passed |
344300 |
16.24 % |
| Transition |
C>T |
Passed |
332160 |
15.66 % |
| Transversion |
A>C |
Passed |
96318 |
4.54 % |
| Transversion |
C>A |
Passed |
103262 |
4.87 % |
| Transversion |
T>G |
Passed |
97028 |
4.58 % |
| Transversion |
G>T |
Passed |
102478 |
4.83 % |
| Transversion |
A>T |
Passed |
91756 |
4.33 % |
| Transversion |
T>A |
Passed |
91854 |
4.33 % |
| Transversion |
C>G |
Passed |
96052 |
4.53 % |
| Transversion |
G>C |
Passed |
96424 |
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 |
2.18 |
9612603 |
4401454 |
| Passed |
1.74 |
1345488 |
775172 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |