/EXTERNAL McGill EMC/variants/K006190_1_lane_gembs
BACK
SAMPLE K006190_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1118194038 |
133252407 |
11.92 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1118194038 |
100% |
1108083406 |
99.10 % |
10110632 |
0.90 % |
| |
|
|
|
|
|
|
| Passed |
136175104 |
12.18 % |
132528254 |
11.96 % |
3646850 |
2.68 % |
| Filtered |
982018934 |
87.82 % |
975555152 |
88.04 % |
6463782 |
4.75 % |
| |
|
|
|
|
|
|
| q20 |
912794039 |
92.95 % |
910244291 |
93.31 % |
2549748 |
39.45 % |
| q20,qd2 |
50315441 |
5.12 % |
46644952 |
4.78 % |
3670489 |
56.79 % |
| q20,mq40 |
14272441 |
1.45 % |
14204209 |
1.46 % |
68232 |
1.06 % |
| q20,qd2,mq40 |
3944829 |
0.40 % |
3883996 |
0.40 % |
60833 |
0.94 % |
| mq40 |
417605 |
0.04 % |
323598 |
0.03 % |
94007 |
1.45 % |
| qd2 |
243409 |
0.02 % |
229379 |
0.02 % |
14030 |
0.22 % |
| qd2,mq40 |
30171 |
0.00 % |
24727 |
0.00 % |
5444 |
0.08 % |
| qd2,fs60,mq40 |
451 |
0.00 % |
0 |
0.00 % |
451 |
0.01 % |
| fs60,mq40 |
211 |
0.00 % |
0 |
0.00 % |
211 |
0.00 % |
| qd2,fs60 |
141 |
0.00 % |
0 |
0.00 % |
141 |
0.00 % |
| q20,qd2,fs60,mq40 |
87 |
0.00 % |
0 |
0.00 % |
87 |
0.00 % |
| fs60 |
61 |
0.00 % |
0 |
0.00 % |
61 |
0.00 % |
| q20,qd2,fs60 |
48 |
0.00 % |
0 |
0.00 % |
48 |
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 |
2947645 |
24.47 % |
| Transition |
G>A |
All |
702910 |
5.84 % |
| Transition |
T>C |
All |
2298606 |
19.09 % |
| Transition |
C>T |
All |
728058 |
6.05 % |
| Transversion |
A>C |
All |
296467 |
2.46 % |
| Transversion |
C>A |
All |
1446448 |
12.01 % |
| Transversion |
T>G |
All |
399751 |
3.32 % |
| Transversion |
G>T |
All |
1388811 |
11.53 % |
| Transversion |
A>T |
All |
579557 |
4.81 % |
| Transversion |
T>A |
All |
661587 |
5.49 % |
| Transversion |
C>G |
All |
326217 |
2.71 % |
| Transversion |
G>C |
All |
267673 |
2.22 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
136581 |
16.03 % |
| Transition |
G>A |
Passed |
135036 |
15.85 % |
| Transition |
T>C |
Passed |
135541 |
15.90 % |
| Transition |
C>T |
Passed |
137366 |
16.12 % |
| Transversion |
A>C |
Passed |
38394 |
4.51 % |
| Transversion |
C>A |
Passed |
40641 |
4.77 % |
| Transversion |
T>G |
Passed |
38636 |
4.53 % |
| Transversion |
G>T |
Passed |
40283 |
4.73 % |
| Transversion |
A>T |
Passed |
32366 |
3.80 % |
| Transversion |
T>A |
Passed |
32444 |
3.81 % |
| Transversion |
C>G |
Passed |
42749 |
5.02 % |
| Transversion |
G>C |
Passed |
42180 |
4.95 % |
| |
|
|
|
|
| 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 |
1.24 |
6677219 |
5366511 |
| Passed |
1.77 |
544524 |
307693 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |