/EXTERNAL McGill EMC/variants/K006174_1_lane_gembs
BACK
SAMPLE K006174_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1136813020 |
117030302 |
10.29 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1136813020 |
100% |
1122174770 |
98.71 % |
14638250 |
1.29 % |
| |
|
|
|
|
|
|
| Passed |
123297433 |
10.85 % |
115982931 |
10.34 % |
7314502 |
5.93 % |
| Filtered |
1013515587 |
89.15 % |
1006191839 |
89.66 % |
7323748 |
5.94 % |
| |
|
|
|
|
|
|
| q20 |
972317789 |
95.94 % |
969436780 |
96.35 % |
2881009 |
39.34 % |
| q20,qd2 |
20225398 |
2.00 % |
16036624 |
1.59 % |
4188774 |
57.19 % |
| q20,mq40 |
15835992 |
1.56 % |
15763448 |
1.57 % |
72544 |
0.99 % |
| q20,qd2,mq40 |
4796263 |
0.47 % |
4736128 |
0.47 % |
60135 |
0.82 % |
| mq40 |
310618 |
0.03 % |
194323 |
0.02 % |
116295 |
1.59 % |
| qd2 |
17894 |
0.00 % |
15558 |
0.00 % |
2336 |
0.03 % |
| qd2,mq40 |
11447 |
0.00 % |
8978 |
0.00 % |
2469 |
0.03 % |
| qd2,fs60,mq40 |
95 |
0.00 % |
0 |
0.00 % |
95 |
0.00 % |
| fs60,mq40 |
52 |
0.00 % |
0 |
0.00 % |
52 |
0.00 % |
| qd2,fs60 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| q20,qd2,fs60,mq40 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| fs60 |
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 |
4188092 |
25.32 % |
| Transition |
G>A |
All |
1062257 |
6.42 % |
| Transition |
T>C |
All |
4114831 |
24.88 % |
| Transition |
C>T |
All |
1056061 |
6.39 % |
| Transversion |
A>C |
All |
296397 |
1.79 % |
| Transversion |
C>A |
All |
1300133 |
7.86 % |
| Transversion |
T>G |
All |
308929 |
1.87 % |
| Transversion |
G>T |
All |
1278388 |
7.73 % |
| Transversion |
A>T |
All |
1150507 |
6.96 % |
| Transversion |
T>A |
All |
1161392 |
7.02 % |
| Transversion |
C>G |
All |
315515 |
1.91 % |
| Transversion |
G>C |
All |
307065 |
1.86 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
164030 |
14.27 % |
| Transition |
G>A |
Passed |
157359 |
13.69 % |
| Transition |
T>C |
Passed |
165051 |
14.36 % |
| Transition |
C>T |
Passed |
158385 |
13.78 % |
| Transversion |
A>C |
Passed |
62498 |
5.44 % |
| Transversion |
C>A |
Passed |
66551 |
5.79 % |
| Transversion |
T>G |
Passed |
62528 |
5.44 % |
| Transversion |
G>T |
Passed |
66550 |
5.79 % |
| Transversion |
A>T |
Passed |
58820 |
5.12 % |
| Transversion |
T>A |
Passed |
58035 |
5.05 % |
| Transversion |
C>G |
Passed |
64655 |
5.62 % |
| Transversion |
G>C |
Passed |
65074 |
5.66 % |
| |
|
|
|
|
| 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 |
1.70 |
10421241 |
6118326 |
| Passed |
1.28 |
644825 |
504711 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |