/EXTERNAL McGill EMC/variants/K006159_1_lane_gembs
BACK
SAMPLE K006159_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156225920 |
714619036 |
61.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156225920 |
100% |
1139262656 |
98.53 % |
16963264 |
1.47 % |
| |
|
|
|
|
|
|
| Passed |
717128824 |
62.02 % |
712071714 |
62.50 % |
5057110 |
0.71 % |
| Filtered |
439097096 |
37.98 % |
427190942 |
37.50 % |
11906154 |
1.66 % |
| |
|
|
|
|
|
|
| q20 |
402367334 |
91.64 % |
399624523 |
93.55 % |
2742811 |
23.04 % |
| q20,qd2 |
16809859 |
3.83 % |
8065217 |
1.89 % |
8744642 |
73.45 % |
| q20,mq40 |
14242813 |
3.24 % |
14127315 |
3.31 % |
115498 |
0.97 % |
| q20,qd2,mq40 |
3621988 |
0.82 % |
3508419 |
0.82 % |
113569 |
0.95 % |
| mq40 |
1338402 |
0.30 % |
1184590 |
0.28 % |
153812 |
1.29 % |
| qd2 |
690858 |
0.16 % |
660292 |
0.15 % |
30566 |
0.26 % |
| qd2,mq40 |
25325 |
0.01 % |
20586 |
0.00 % |
4739 |
0.04 % |
| qd2,fs60,mq40 |
249 |
0.00 % |
0 |
0.00 % |
249 |
0.00 % |
| fs60,mq40 |
123 |
0.00 % |
0 |
0.00 % |
123 |
0.00 % |
| qd2,fs60 |
94 |
0.00 % |
0 |
0.00 % |
94 |
0.00 % |
| q20,qd2,fs60,mq40 |
28 |
0.00 % |
0 |
0.00 % |
28 |
0.00 % |
| fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
5973249 |
32.15 % |
| Transition |
G>A |
All |
1355636 |
7.30 % |
| Transition |
T>C |
All |
5456710 |
29.37 % |
| Transition |
C>T |
All |
1395145 |
7.51 % |
| Transversion |
A>C |
All |
334699 |
1.80 % |
| Transversion |
C>A |
All |
974071 |
5.24 % |
| Transversion |
T>G |
All |
354316 |
1.91 % |
| Transversion |
G>T |
All |
907242 |
4.88 % |
| Transversion |
A>T |
All |
581461 |
3.13 % |
| Transversion |
T>A |
All |
627533 |
3.38 % |
| Transversion |
C>G |
All |
315251 |
1.70 % |
| Transversion |
G>C |
All |
301461 |
1.62 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
561506 |
17.31 % |
| Transition |
G>A |
Passed |
503185 |
15.51 % |
| Transition |
T>C |
Passed |
578831 |
17.84 % |
| Transition |
C>T |
Passed |
509940 |
15.72 % |
| Transversion |
A>C |
Passed |
136592 |
4.21 % |
| Transversion |
C>A |
Passed |
143365 |
4.42 % |
| Transversion |
T>G |
Passed |
136916 |
4.22 % |
| Transversion |
G>T |
Passed |
143632 |
4.43 % |
| Transversion |
A>T |
Passed |
121396 |
3.74 % |
| Transversion |
T>A |
Passed |
120760 |
3.72 % |
| Transversion |
C>G |
Passed |
143473 |
4.42 % |
| Transversion |
G>C |
Passed |
144087 |
4.44 % |
| |
|
|
|
|
| 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 |
3.23 |
14180740 |
4396034 |
| Passed |
1.98 |
2153462 |
1090221 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |