/EXTERNAL McGill EMC/variants/K006208_1_lane_gembs
BACK
SAMPLE K006208_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1139593921 |
219873867 |
19.29 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1139593921 |
100% |
1127427933 |
98.93 % |
12165988 |
1.07 % |
| |
|
|
|
|
|
|
| Passed |
223552072 |
19.62 % |
218751623 |
19.40 % |
4800449 |
2.15 % |
| Filtered |
916041849 |
80.38 % |
908676310 |
80.60 % |
7365539 |
3.29 % |
| |
|
|
|
|
|
|
| q20 |
876247460 |
95.66 % |
873143087 |
96.09 % |
3104373 |
42.15 % |
| q20,qd2 |
20815278 |
2.27 % |
16808657 |
1.85 % |
4006621 |
54.40 % |
| q20,mq40 |
14800209 |
1.62 % |
14725484 |
1.62 % |
74725 |
1.01 % |
| q20,qd2,mq40 |
3532883 |
0.39 % |
3475057 |
0.38 % |
57826 |
0.79 % |
| mq40 |
519563 |
0.06 % |
409847 |
0.05 % |
109716 |
1.49 % |
| qd2 |
102785 |
0.01 % |
95225 |
0.01 % |
7560 |
0.10 % |
| qd2,mq40 |
23207 |
0.00 % |
18953 |
0.00 % |
4254 |
0.06 % |
| qd2,fs60,mq40 |
211 |
0.00 % |
0 |
0.00 % |
211 |
0.00 % |
| fs60,mq40 |
128 |
0.00 % |
0 |
0.00 % |
128 |
0.00 % |
| qd2,fs60 |
79 |
0.00 % |
0 |
0.00 % |
79 |
0.00 % |
| fs60 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| q20,qd2,fs60,mq40 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3928539 |
28.05 % |
| Transition |
G>A |
All |
1308829 |
9.35 % |
| Transition |
T>C |
All |
2760164 |
19.71 % |
| Transition |
C>T |
All |
1352555 |
9.66 % |
| Transversion |
A>C |
All |
333807 |
2.38 % |
| Transversion |
C>A |
All |
910360 |
6.50 % |
| Transversion |
T>G |
All |
503630 |
3.60 % |
| Transversion |
G>T |
All |
815017 |
5.82 % |
| Transversion |
A>T |
All |
653022 |
4.66 % |
| Transversion |
T>A |
All |
813252 |
5.81 % |
| Transversion |
C>G |
All |
359107 |
2.56 % |
| Transversion |
G>C |
All |
265354 |
1.89 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
209111 |
15.74 % |
| Transition |
G>A |
Passed |
198099 |
14.92 % |
| Transition |
T>C |
Passed |
207297 |
15.61 % |
| Transition |
C>T |
Passed |
201099 |
15.14 % |
| Transversion |
A>C |
Passed |
64206 |
4.83 % |
| Transversion |
C>A |
Passed |
66609 |
5.02 % |
| Transversion |
T>G |
Passed |
64774 |
4.88 % |
| Transversion |
G>T |
Passed |
66712 |
5.02 % |
| Transversion |
A>T |
Passed |
54136 |
4.08 % |
| Transversion |
T>A |
Passed |
53682 |
4.04 % |
| Transversion |
C>G |
Passed |
71179 |
5.36 % |
| Transversion |
G>C |
Passed |
71282 |
5.37 % |
| |
|
|
|
|
| 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 |
2.01 |
9350087 |
4653549 |
| Passed |
1.59 |
815606 |
512580 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |