/EXTERNAL McGill EMC/variants/K006138_1_lane_gembs
BACK
SAMPLE K006138_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1176523701 |
477484118 |
40.58 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1176523701 |
100% |
1116792162 |
94.92 % |
59731539 |
5.08 % |
| |
|
|
|
|
|
|
| Passed |
489185712 |
41.58 % |
471067563 |
42.18 % |
18118149 |
3.70 % |
| Filtered |
687337989 |
58.42 % |
645724599 |
57.82 % |
41613390 |
8.51 % |
| |
|
|
|
|
|
|
| q20 |
593725642 |
86.38 % |
586175223 |
90.78 % |
7550419 |
18.14 % |
| q20,qd2 |
40402854 |
5.88 % |
14711446 |
2.28 % |
25691408 |
61.74 % |
| q20,mq40 |
25057192 |
3.65 % |
24017089 |
3.72 % |
1040103 |
2.50 % |
| mq40 |
17850700 |
2.60 % |
14094124 |
2.18 % |
3756576 |
9.03 % |
| q20,qd2,mq40 |
8117203 |
1.18 % |
5139189 |
0.80 % |
2978014 |
7.16 % |
| qd2 |
1870680 |
0.27 % |
1382217 |
0.21 % |
488463 |
1.17 % |
| qd2,mq40 |
312952 |
0.05 % |
205311 |
0.03 % |
107641 |
0.26 % |
| qd2,fs60,mq40 |
468 |
0.00 % |
0 |
0.00 % |
468 |
0.00 % |
| fs60,mq40 |
184 |
0.00 % |
0 |
0.00 % |
184 |
0.00 % |
| qd2,fs60 |
62 |
0.00 % |
0 |
0.00 % |
62 |
0.00 % |
| q20,qd2,fs60,mq40 |
36 |
0.00 % |
0 |
0.00 % |
36 |
0.00 % |
| fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
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 |
15330366 |
24.83 % |
| Transition |
G>A |
All |
6440844 |
10.43 % |
| Transition |
T>C |
All |
14839747 |
24.03 % |
| Transition |
C>T |
All |
6059193 |
9.81 % |
| Transversion |
A>C |
All |
1196801 |
1.94 % |
| Transversion |
C>A |
All |
4577878 |
7.41 % |
| Transversion |
T>G |
All |
1262397 |
2.04 % |
| Transversion |
G>T |
All |
4620699 |
7.48 % |
| Transversion |
A>T |
All |
2568351 |
4.16 % |
| Transversion |
T>A |
All |
2496576 |
4.04 % |
| Transversion |
C>G |
All |
1199874 |
1.94 % |
| Transversion |
G>C |
All |
1156635 |
1.87 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1591618 |
23.37 % |
| Transition |
G>A |
Passed |
850584 |
12.49 % |
| Transition |
T>C |
Passed |
1497474 |
21.99 % |
| Transition |
C>T |
Passed |
809464 |
11.88 % |
| Transversion |
A>C |
Passed |
288042 |
4.23 % |
| Transversion |
C>A |
Passed |
219864 |
3.23 % |
| Transversion |
T>G |
Passed |
292552 |
4.30 % |
| Transversion |
G>T |
Passed |
219217 |
3.22 % |
| Transversion |
A>T |
Passed |
220844 |
3.24 % |
| Transversion |
T>A |
Passed |
221440 |
3.25 % |
| Transversion |
C>G |
Passed |
300816 |
4.42 % |
| Transversion |
G>C |
Passed |
299337 |
4.39 % |
| |
|
|
|
|
| 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 |
2.24 |
42670150 |
19079211 |
| Passed |
2.30 |
4749140 |
2062112 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |