/EXTERNAL McGill EMC/variants/K006143_1_lane_gembs
BACK
SAMPLE K006143_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1150249765 |
870978872 |
75.72 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1150249765 |
100% |
1134987001 |
98.67 % |
15262764 |
1.33 % |
| |
|
|
|
|
|
|
| Passed |
872987444 |
75.90 % |
868717426 |
76.54 % |
4270018 |
0.49 % |
| Filtered |
277262321 |
24.10 % |
266269575 |
23.46 % |
10992746 |
1.26 % |
| |
|
|
|
|
|
|
| q20 |
243036062 |
87.66 % |
241580950 |
90.73 % |
1455112 |
13.24 % |
| q20,qd2 |
15287133 |
5.51 % |
6115548 |
2.30 % |
9171585 |
83.43 % |
| q20,mq40 |
13325141 |
4.81 % |
13237808 |
4.97 % |
87333 |
0.79 % |
| q20,qd2,mq40 |
3418853 |
1.23 % |
3322626 |
1.25 % |
96227 |
0.88 % |
| mq40 |
1456736 |
0.53 % |
1307825 |
0.49 % |
148911 |
1.35 % |
| qd2 |
716004 |
0.26 % |
687455 |
0.26 % |
28549 |
0.26 % |
| qd2,mq40 |
22013 |
0.01 % |
17363 |
0.01 % |
4650 |
0.04 % |
| qd2,fs60,mq40 |
169 |
0.00 % |
0 |
0.00 % |
169 |
0.00 % |
| fs60,mq40 |
92 |
0.00 % |
0 |
0.00 % |
92 |
0.00 % |
| qd2,fs60 |
84 |
0.00 % |
0 |
0.00 % |
84 |
0.00 % |
| q20,qd2,fs60,mq40 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
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 |
5799167 |
34.37 % |
| Transition |
G>A |
All |
1216669 |
7.21 % |
| Transition |
T>C |
All |
5731296 |
33.97 % |
| Transition |
C>T |
All |
1228012 |
7.28 % |
| Transversion |
A>C |
All |
217276 |
1.29 % |
| Transversion |
C>A |
All |
610149 |
3.62 % |
| Transversion |
T>G |
All |
221387 |
1.31 % |
| Transversion |
G>T |
All |
592192 |
3.51 % |
| Transversion |
A>T |
All |
418775 |
2.48 % |
| Transversion |
T>A |
All |
410112 |
2.43 % |
| Transversion |
C>G |
All |
213618 |
1.27 % |
| Transversion |
G>C |
All |
211688 |
1.25 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
545335 |
16.99 % |
| Transition |
G>A |
Passed |
512324 |
15.96 % |
| Transition |
T>C |
Passed |
542768 |
16.91 % |
| Transition |
C>T |
Passed |
514895 |
16.04 % |
| Transversion |
A>C |
Passed |
135979 |
4.24 % |
| Transversion |
C>A |
Passed |
146678 |
4.57 % |
| Transversion |
T>G |
Passed |
137311 |
4.28 % |
| Transversion |
G>T |
Passed |
146351 |
4.56 % |
| Transversion |
A>T |
Passed |
125502 |
3.91 % |
| Transversion |
T>A |
Passed |
126063 |
3.93 % |
| Transversion |
C>G |
Passed |
138167 |
4.30 % |
| Transversion |
G>C |
Passed |
139120 |
4.33 % |
| |
|
|
|
|
| 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 |
4.83 |
13975144 |
2895197 |
| Passed |
1.93 |
2115322 |
1095171 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |