/EXTERNAL McGill EMC/variants/K006175_1_lane_gembs
BACK
SAMPLE K006175_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1151321509 |
952578850 |
82.74 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1151321509 |
100% |
1138466622 |
98.88 % |
12854887 |
1.12 % |
| |
|
|
|
|
|
|
| Passed |
953480224 |
82.82 % |
950151307 |
83.46 % |
3328917 |
0.35 % |
| Filtered |
197841285 |
17.18 % |
188315315 |
16.54 % |
9525970 |
1.00 % |
| |
|
|
|
|
|
|
| q20 |
161424577 |
81.59 % |
160067017 |
85.00 % |
1357560 |
14.25 % |
| q20,mq40 |
14689089 |
7.42 % |
14545087 |
7.72 % |
144002 |
1.51 % |
| q20,qd2 |
13983552 |
7.07 % |
6371979 |
3.38 % |
7611573 |
79.90 % |
| q20,qd2,mq40 |
3689806 |
1.87 % |
3539522 |
1.88 % |
150284 |
1.58 % |
| mq40 |
2225798 |
1.13 % |
2052624 |
1.09 % |
173174 |
1.82 % |
| qd2 |
1799971 |
0.91 % |
1716691 |
0.91 % |
83280 |
0.87 % |
| qd2,mq40 |
27958 |
0.01 % |
22395 |
0.01 % |
5563 |
0.06 % |
| qd2,fs60,mq40 |
289 |
0.00 % |
0 |
0.00 % |
289 |
0.00 % |
| fs60,mq40 |
114 |
0.00 % |
0 |
0.00 % |
114 |
0.00 % |
| qd2,fs60 |
73 |
0.00 % |
0 |
0.00 % |
73 |
0.00 % |
| q20,qd2,fs60,mq40 |
31 |
0.00 % |
0 |
0.00 % |
31 |
0.00 % |
| fs60 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| q20,qd2,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
4491626 |
30.97 % |
| Transition |
G>A |
All |
1227540 |
8.46 % |
| Transition |
T>C |
All |
4369105 |
30.12 % |
| Transition |
C>T |
All |
1248879 |
8.61 % |
| Transversion |
A>C |
All |
255166 |
1.76 % |
| Transversion |
C>A |
All |
710238 |
4.90 % |
| Transversion |
T>G |
All |
252812 |
1.74 % |
| Transversion |
G>T |
All |
661505 |
4.56 % |
| Transversion |
A>T |
All |
397962 |
2.74 % |
| Transversion |
T>A |
All |
412485 |
2.84 % |
| Transversion |
C>G |
All |
238311 |
1.64 % |
| Transversion |
G>C |
All |
239380 |
1.65 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
611151 |
17.53 % |
| Transition |
G>A |
Passed |
557781 |
16.00 % |
| Transition |
T>C |
Passed |
624229 |
17.90 % |
| Transition |
C>T |
Passed |
567764 |
16.28 % |
| Transversion |
A>C |
Passed |
140843 |
4.04 % |
| Transversion |
C>A |
Passed |
150257 |
4.31 % |
| Transversion |
T>G |
Passed |
141125 |
4.05 % |
| Transversion |
G>T |
Passed |
149165 |
4.28 % |
| Transversion |
A>T |
Passed |
127843 |
3.67 % |
| Transversion |
T>A |
Passed |
127924 |
3.67 % |
| Transversion |
C>G |
Passed |
144204 |
4.14 % |
| Transversion |
G>C |
Passed |
144807 |
4.15 % |
| |
|
|
|
|
| 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 |
3.58 |
11337150 |
3167859 |
| Passed |
2.10 |
2360925 |
1126168 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |