/EXTERNAL McGill EMC/variants/K006211_1_lane_gembs
BACK
SAMPLE K006211_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1161098530 |
922240627 |
79.43 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1161098530 |
100% |
1142027997 |
98.36 % |
19070533 |
1.64 % |
| |
|
|
|
|
|
|
| Passed |
924100969 |
79.59 % |
918020564 |
80.39 % |
6080405 |
0.66 % |
| Filtered |
236997561 |
20.41 % |
224007433 |
19.61 % |
12990128 |
1.41 % |
| |
|
|
|
|
|
|
| q20 |
194540173 |
82.09 % |
192778877 |
86.06 % |
1761296 |
13.56 % |
| q20,qd2 |
17893634 |
7.55 % |
7516424 |
3.36 % |
10377210 |
79.89 % |
| q20,mq40 |
14543062 |
6.14 % |
14425649 |
6.44 % |
117413 |
0.90 % |
| mq40 |
3644957 |
1.54 % |
3408885 |
1.52 % |
236072 |
1.82 % |
| qd2 |
3384352 |
1.43 % |
3112959 |
1.39 % |
271393 |
2.09 % |
| q20,qd2,mq40 |
2953155 |
1.25 % |
2734656 |
1.22 % |
218499 |
1.68 % |
| qd2,mq40 |
37122 |
0.02 % |
29983 |
0.01 % |
7139 |
0.05 % |
| qd2,fs60,mq40 |
501 |
0.00 % |
0 |
0.00 % |
501 |
0.00 % |
| qd2,fs60 |
245 |
0.00 % |
0 |
0.00 % |
245 |
0.00 % |
| fs60,mq40 |
198 |
0.00 % |
0 |
0.00 % |
198 |
0.00 % |
| fs60 |
94 |
0.00 % |
0 |
0.00 % |
94 |
0.00 % |
| q20,qd2,fs60,mq40 |
51 |
0.00 % |
0 |
0.00 % |
51 |
0.00 % |
| q20,qd2,fs60 |
16 |
0.00 % |
0 |
0.00 % |
16 |
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 |
6551100 |
32.93 % |
| Transition |
G>A |
All |
1377902 |
6.93 % |
| Transition |
T>C |
All |
6413052 |
32.24 % |
| Transition |
C>T |
All |
1380520 |
6.94 % |
| Transversion |
A>C |
All |
271259 |
1.36 % |
| Transversion |
C>A |
All |
1073788 |
5.40 % |
| Transversion |
T>G |
All |
275611 |
1.39 % |
| Transversion |
G>T |
All |
1064954 |
5.35 % |
| Transversion |
A>T |
All |
456906 |
2.30 % |
| Transversion |
T>A |
All |
445116 |
2.24 % |
| Transversion |
C>G |
All |
292839 |
1.47 % |
| Transversion |
G>C |
All |
289747 |
1.46 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
794668 |
17.12 % |
| Transition |
G>A |
Passed |
727040 |
15.66 % |
| Transition |
T>C |
Passed |
793072 |
17.09 % |
| Transition |
C>T |
Passed |
735441 |
15.84 % |
| Transversion |
A>C |
Passed |
195717 |
4.22 % |
| Transversion |
C>A |
Passed |
212937 |
4.59 % |
| Transversion |
T>G |
Passed |
195349 |
4.21 % |
| Transversion |
G>T |
Passed |
213349 |
4.60 % |
| Transversion |
A>T |
Passed |
185195 |
3.99 % |
| Transversion |
T>A |
Passed |
184899 |
3.98 % |
| Transversion |
C>G |
Passed |
201725 |
4.35 % |
| Transversion |
G>C |
Passed |
202128 |
4.35 % |
| |
|
|
|
|
| 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 |
3.77 |
15722574 |
4170220 |
| Passed |
1.92 |
3050221 |
1591299 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |