/EXTERNAL McGill EMC/variants/K006198_1_lane_gembs
BACK
SAMPLE K006198_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1160866724 |
983891069 |
84.75 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1160866724 |
100% |
1142862173 |
98.45 % |
18004551 |
1.55 % |
| |
|
|
|
|
|
|
| Passed |
985368011 |
84.88 % |
979486646 |
85.70 % |
5881365 |
0.60 % |
| Filtered |
175498713 |
15.12 % |
163375527 |
14.30 % |
12123186 |
1.23 % |
| |
|
|
|
|
|
|
| q20 |
138498428 |
78.92 % |
137054574 |
83.89 % |
1443854 |
11.91 % |
| q20,qd2 |
15477693 |
8.82 % |
5629813 |
3.45 % |
9847880 |
81.23 % |
| q20,mq40 |
12985921 |
7.40 % |
12882526 |
7.89 % |
103395 |
0.85 % |
| mq40 |
3287348 |
1.87 % |
3067010 |
1.88 % |
220338 |
1.82 % |
| q20,qd2,mq40 |
2853929 |
1.63 % |
2680685 |
1.64 % |
173244 |
1.43 % |
| qd2 |
2365436 |
1.35 % |
2037532 |
1.25 % |
327904 |
2.70 % |
| qd2,mq40 |
29171 |
0.02 % |
23387 |
0.01 % |
5784 |
0.05 % |
| qd2,fs60,mq40 |
340 |
0.00 % |
0 |
0.00 % |
340 |
0.00 % |
| qd2,fs60 |
173 |
0.00 % |
0 |
0.00 % |
173 |
0.00 % |
| fs60,mq40 |
132 |
0.00 % |
0 |
0.00 % |
132 |
0.00 % |
| fs60 |
82 |
0.00 % |
0 |
0.00 % |
82 |
0.00 % |
| q20,qd2,fs60,mq40 |
37 |
0.00 % |
0 |
0.00 % |
37 |
0.00 % |
| q20,qd2,fs60 |
22 |
0.00 % |
0 |
0.00 % |
22 |
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 |
6387382 |
33.95 % |
| Transition |
G>A |
All |
1320529 |
7.02 % |
| Transition |
T>C |
All |
6288425 |
33.42 % |
| Transition |
C>T |
All |
1320466 |
7.02 % |
| Transversion |
A>C |
All |
275094 |
1.46 % |
| Transversion |
C>A |
All |
751874 |
4.00 % |
| Transversion |
T>G |
All |
278190 |
1.48 % |
| Transversion |
G>T |
All |
744469 |
3.96 % |
| Transversion |
A>T |
All |
445710 |
2.37 % |
| Transversion |
T>A |
All |
432011 |
2.30 % |
| Transversion |
C>G |
All |
286235 |
1.52 % |
| Transversion |
G>C |
All |
284360 |
1.51 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
831756 |
17.16 % |
| Transition |
G>A |
Passed |
764507 |
15.77 % |
| Transition |
T>C |
Passed |
832791 |
17.18 % |
| Transition |
C>T |
Passed |
772911 |
15.94 % |
| Transversion |
A>C |
Passed |
203507 |
4.20 % |
| Transversion |
C>A |
Passed |
219876 |
4.53 % |
| Transversion |
T>G |
Passed |
203703 |
4.20 % |
| Transversion |
G>T |
Passed |
220110 |
4.54 % |
| Transversion |
A>T |
Passed |
189691 |
3.91 % |
| Transversion |
T>A |
Passed |
189053 |
3.90 % |
| Transversion |
C>G |
Passed |
210371 |
4.34 % |
| Transversion |
G>C |
Passed |
210189 |
4.34 % |
| |
|
|
|
|
| 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 |
4.38 |
15316802 |
3497943 |
| Passed |
1.94 |
3201965 |
1646500 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |