/EXTERNAL McGill EMC/variants/K006132_1_lane_gembs
BACK
SAMPLE K006132_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1150670284 |
757827174 |
65.86 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1150670284 |
100% |
1141266212 |
99.18 % |
9404072 |
0.82 % |
| |
|
|
|
|
|
|
| Passed |
759084761 |
65.97 % |
755777650 |
66.22 % |
3307111 |
0.44 % |
| Filtered |
391585523 |
34.03 % |
385488562 |
33.78 % |
6096961 |
0.80 % |
| |
|
|
|
|
|
|
| q20 |
362727438 |
92.63 % |
361457255 |
93.77 % |
1270183 |
20.83 % |
| q20,mq40 |
11836678 |
3.02 % |
11749974 |
3.05 % |
86704 |
1.42 % |
| q20,qd2 |
11404703 |
2.91 % |
6917588 |
1.79 % |
4487115 |
73.60 % |
| q20,qd2,mq40 |
3071959 |
0.78 % |
2989358 |
0.78 % |
82601 |
1.35 % |
| mq40 |
1312909 |
0.34 % |
1186611 |
0.31 % |
126298 |
2.07 % |
| qd2 |
1193498 |
0.30 % |
1157602 |
0.30 % |
35896 |
0.59 % |
| qd2,mq40 |
37358 |
0.01 % |
30174 |
0.01 % |
7184 |
0.12 % |
| qd2,fs60,mq40 |
538 |
0.00 % |
0 |
0.00 % |
538 |
0.01 % |
| fs60,mq40 |
232 |
0.00 % |
0 |
0.00 % |
232 |
0.00 % |
| qd2,fs60 |
130 |
0.00 % |
0 |
0.00 % |
130 |
0.00 % |
| fs60 |
43 |
0.00 % |
0 |
0.00 % |
43 |
0.00 % |
| q20,qd2,fs60,mq40 |
28 |
0.00 % |
0 |
0.00 % |
28 |
0.00 % |
| q20,qd2,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
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 |
3048826 |
27.51 % |
| Transition |
G>A |
All |
1090895 |
9.84 % |
| Transition |
T>C |
All |
2951030 |
26.63 % |
| Transition |
C>T |
All |
1105670 |
9.98 % |
| Transversion |
A>C |
All |
235966 |
2.13 % |
| Transversion |
C>A |
All |
603338 |
5.44 % |
| Transversion |
T>G |
All |
239029 |
2.16 % |
| Transversion |
G>T |
All |
594409 |
5.36 % |
| Transversion |
A>T |
All |
369920 |
3.34 % |
| Transversion |
T>A |
All |
370314 |
3.34 % |
| Transversion |
C>G |
All |
238081 |
2.15 % |
| Transversion |
G>C |
All |
235379 |
2.12 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
483659 |
16.59 % |
| Transition |
G>A |
Passed |
469005 |
16.09 % |
| Transition |
T>C |
Passed |
488735 |
16.77 % |
| Transition |
C>T |
Passed |
473808 |
16.26 % |
| Transversion |
A>C |
Passed |
124683 |
4.28 % |
| Transversion |
C>A |
Passed |
133632 |
4.58 % |
| Transversion |
T>G |
Passed |
125053 |
4.29 % |
| Transversion |
G>T |
Passed |
131822 |
4.52 % |
| Transversion |
A>T |
Passed |
114531 |
3.93 % |
| Transversion |
T>A |
Passed |
115222 |
3.95 % |
| Transversion |
C>G |
Passed |
127350 |
4.37 % |
| Transversion |
G>C |
Passed |
127311 |
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 |
2.84 |
8196421 |
2886436 |
| Passed |
1.92 |
1915207 |
999604 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |