/EXTERNAL McGill EMC/variants/K006151_1_lane_gembs
BACK
SAMPLE K006151_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1144635887 |
806176066 |
70.43 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1144635887 |
100% |
1134841583 |
99.14 % |
9794304 |
0.86 % |
| |
|
|
|
|
|
|
| Passed |
807388716 |
70.54 % |
804066457 |
70.85 % |
3322259 |
0.41 % |
| Filtered |
337247171 |
29.46 % |
330775126 |
29.15 % |
6472045 |
0.80 % |
| |
|
|
|
|
|
|
| q20 |
305190183 |
90.49 % |
304117587 |
91.94 % |
1072596 |
16.57 % |
| q20,qd2 |
13306573 |
3.95 % |
8259044 |
2.50 % |
5047529 |
77.99 % |
| q20,mq40 |
11400245 |
3.38 % |
11320905 |
3.42 % |
79340 |
1.23 % |
| qd2 |
2896763 |
0.86 % |
2859227 |
0.86 % |
37536 |
0.58 % |
| q20,qd2,mq40 |
2807695 |
0.83 % |
2712145 |
0.82 % |
95550 |
1.48 % |
| mq40 |
1606606 |
0.48 % |
1475434 |
0.45 % |
131172 |
2.03 % |
| qd2,mq40 |
37839 |
0.01 % |
30784 |
0.01 % |
7055 |
0.11 % |
| qd2,fs60,mq40 |
658 |
0.00 % |
0 |
0.00 % |
658 |
0.01 % |
| qd2,fs60 |
223 |
0.00 % |
0 |
0.00 % |
223 |
0.00 % |
| fs60,mq40 |
216 |
0.00 % |
0 |
0.00 % |
216 |
0.00 % |
| fs60 |
96 |
0.00 % |
0 |
0.00 % |
96 |
0.00 % |
| q20,qd2,fs60,mq40 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| q20,qd2,fs60 |
28 |
0.00 % |
0 |
0.00 % |
28 |
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 |
2897975 |
25.34 % |
| Transition |
G>A |
All |
1161596 |
10.16 % |
| Transition |
T>C |
All |
2777128 |
24.28 % |
| Transition |
C>T |
All |
1173698 |
10.26 % |
| Transversion |
A>C |
All |
222627 |
1.95 % |
| Transversion |
C>A |
All |
954619 |
8.35 % |
| Transversion |
T>G |
All |
227608 |
1.99 % |
| Transversion |
G>T |
All |
958596 |
8.38 % |
| Transversion |
A>T |
All |
308334 |
2.70 % |
| Transversion |
T>A |
All |
308164 |
2.69 % |
| Transversion |
C>G |
All |
224359 |
1.96 % |
| Transversion |
G>C |
All |
221538 |
1.94 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
497977 |
16.55 % |
| Transition |
G>A |
Passed |
487338 |
16.20 % |
| Transition |
T>C |
Passed |
500180 |
16.62 % |
| Transition |
C>T |
Passed |
491113 |
16.32 % |
| Transversion |
A>C |
Passed |
129321 |
4.30 % |
| Transversion |
C>A |
Passed |
137573 |
4.57 % |
| Transversion |
T>G |
Passed |
129853 |
4.32 % |
| Transversion |
G>T |
Passed |
136250 |
4.53 % |
| Transversion |
A>T |
Passed |
117368 |
3.90 % |
| Transversion |
T>A |
Passed |
116924 |
3.89 % |
| Transversion |
C>G |
Passed |
132255 |
4.40 % |
| Transversion |
G>C |
Passed |
132951 |
4.42 % |
| |
|
|
|
|
| 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 |
2.34 |
8010397 |
3425845 |
| Passed |
1.91 |
1976608 |
1032495 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |