/EXTERNAL McGill EMC/variants/K006202_1_lane_gembs
BACK
SAMPLE K006202_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1161048478 |
891857946 |
76.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1161048478 |
100% |
1139973126 |
98.18 % |
21075352 |
1.82 % |
| |
|
|
|
|
|
|
| Passed |
894041116 |
77.00 % |
887881439 |
77.89 % |
6159677 |
0.69 % |
| Filtered |
267007362 |
23.00 % |
252091687 |
22.11 % |
14915675 |
1.67 % |
| |
|
|
|
|
|
|
| q20 |
224493645 |
84.08 % |
222407643 |
88.22 % |
2086002 |
13.99 % |
| q20,qd2 |
21041917 |
7.88 % |
8881206 |
3.52 % |
12160711 |
81.53 % |
| q20,mq40 |
13389739 |
5.01 % |
13281057 |
5.27 % |
108682 |
0.73 % |
| q20,qd2,mq40 |
3150994 |
1.18 % |
2977436 |
1.18 % |
173558 |
1.16 % |
| qd2 |
2760201 |
1.03 % |
2579266 |
1.02 % |
180935 |
1.21 % |
| mq40 |
2145537 |
0.80 % |
1945086 |
0.77 % |
200451 |
1.34 % |
| qd2,mq40 |
24683 |
0.01 % |
19993 |
0.01 % |
4690 |
0.03 % |
| qd2,fs60,mq40 |
296 |
0.00 % |
0 |
0.00 % |
296 |
0.00 % |
| fs60,mq40 |
143 |
0.00 % |
0 |
0.00 % |
143 |
0.00 % |
| qd2,fs60 |
122 |
0.00 % |
0 |
0.00 % |
122 |
0.00 % |
| fs60 |
43 |
0.00 % |
0 |
0.00 % |
43 |
0.00 % |
| q20,qd2,fs60,mq40 |
30 |
0.00 % |
0 |
0.00 % |
30 |
0.00 % |
| q20,qd2,fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
7324751 |
33.28 % |
| Transition |
G>A |
All |
1338248 |
6.08 % |
| Transition |
T>C |
All |
7259140 |
32.98 % |
| Transition |
C>T |
All |
1338697 |
6.08 % |
| Transversion |
A>C |
All |
271704 |
1.23 % |
| Transversion |
C>A |
All |
1324427 |
6.02 % |
| Transversion |
T>G |
All |
274034 |
1.25 % |
| Transversion |
G>T |
All |
1315288 |
5.98 % |
| Transversion |
A>T |
All |
501659 |
2.28 % |
| Transversion |
T>A |
All |
485945 |
2.21 % |
| Transversion |
C>G |
All |
288310 |
1.31 % |
| Transversion |
G>C |
All |
286456 |
1.30 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
760113 |
17.06 % |
| Transition |
G>A |
Passed |
695693 |
15.62 % |
| Transition |
T>C |
Passed |
761098 |
17.09 % |
| Transition |
C>T |
Passed |
701061 |
15.74 % |
| Transversion |
A>C |
Passed |
189875 |
4.26 % |
| Transversion |
C>A |
Passed |
205521 |
4.61 % |
| Transversion |
T>G |
Passed |
190267 |
4.27 % |
| Transversion |
G>T |
Passed |
205864 |
4.62 % |
| Transversion |
A>T |
Passed |
177936 |
3.99 % |
| Transversion |
T>A |
Passed |
177501 |
3.98 % |
| Transversion |
C>G |
Passed |
194712 |
4.37 % |
| Transversion |
G>C |
Passed |
194876 |
4.37 % |
| |
|
|
|
|
| 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 |
3.64 |
17260836 |
4747823 |
| Passed |
1.90 |
2917965 |
1536552 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |