/EXTERNAL McGill EMC/variants/K006201_1_lane_gembs
BACK
SAMPLE K006201_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1174182095 |
1079031968 |
91.90 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1174182095 |
100% |
1154953924 |
98.36 % |
19228171 |
1.64 % |
| |
|
|
|
|
|
|
| Passed |
1079963556 |
91.98 % |
1075402873 |
93.11 % |
4560683 |
0.42 % |
| Filtered |
94218539 |
8.02 % |
79551051 |
6.89 % |
14667488 |
1.36 % |
| |
|
|
|
|
|
|
| q20 |
48818211 |
51.81 % |
47508164 |
59.72 % |
1310047 |
8.93 % |
| q20,qd2 |
17215655 |
18.27 % |
6070846 |
7.63 % |
11144809 |
75.98 % |
| q20,mq40 |
11955666 |
12.69 % |
11724184 |
14.74 % |
231482 |
1.58 % |
| qd2 |
8030370 |
8.52 % |
6727734 |
8.46 % |
1302636 |
8.88 % |
| mq40 |
5309272 |
5.64 % |
4997169 |
6.28 % |
312103 |
2.13 % |
| q20,qd2,mq40 |
2811014 |
2.98 % |
2457904 |
3.09 % |
353110 |
2.41 % |
| qd2,mq40 |
77135 |
0.08 % |
65050 |
0.08 % |
12085 |
0.08 % |
| qd2,fs60,mq40 |
511 |
0.00 % |
0 |
0.00 % |
511 |
0.00 % |
| qd2,fs60 |
290 |
0.00 % |
0 |
0.00 % |
290 |
0.00 % |
| fs60,mq40 |
204 |
0.00 % |
0 |
0.00 % |
204 |
0.00 % |
| fs60 |
118 |
0.00 % |
0 |
0.00 % |
118 |
0.00 % |
| q20,qd2,fs60,mq40 |
50 |
0.00 % |
0 |
0.00 % |
50 |
0.00 % |
| q20,qd2,fs60 |
40 |
0.00 % |
0 |
0.00 % |
40 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
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 |
7320020 |
34.93 % |
| Transition |
G>A |
All |
1184225 |
5.65 % |
| Transition |
T>C |
All |
6963882 |
33.23 % |
| Transition |
C>T |
All |
1204390 |
5.75 % |
| Transversion |
A>C |
All |
340728 |
1.63 % |
| Transversion |
C>A |
All |
853316 |
4.07 % |
| Transversion |
T>G |
All |
349494 |
1.67 % |
| Transversion |
G>T |
All |
851547 |
4.06 % |
| Transversion |
A>T |
All |
629170 |
3.00 % |
| Transversion |
T>A |
All |
632397 |
3.02 % |
| Transversion |
C>G |
All |
315898 |
1.51 % |
| Transversion |
G>C |
All |
309775 |
1.48 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1154414 |
23.67 % |
| Transition |
G>A |
Passed |
629803 |
12.91 % |
| Transition |
T>C |
Passed |
1108336 |
22.73 % |
| Transition |
C>T |
Passed |
631535 |
12.95 % |
| Transversion |
A>C |
Passed |
174585 |
3.58 % |
| Transversion |
C>A |
Passed |
175312 |
3.59 % |
| Transversion |
T>G |
Passed |
175840 |
3.61 % |
| Transversion |
G>T |
Passed |
173645 |
3.56 % |
| Transversion |
A>T |
Passed |
156089 |
3.20 % |
| Transversion |
T>A |
Passed |
156159 |
3.20 % |
| Transversion |
C>G |
Passed |
170658 |
3.50 % |
| Transversion |
G>C |
Passed |
170561 |
3.50 % |
| |
|
|
|
|
| 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 |
3.89 |
16672517 |
4282325 |
| Passed |
2.60 |
3524088 |
1352849 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |