/EXTERNAL McGill EMC/variants/K006149_1_lane_gembs
BACK
SAMPLE K006149_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1151594101 |
718400367 |
62.38 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1151594101 |
100% |
1140010794 |
98.99 % |
11583307 |
1.01 % |
| |
|
|
|
|
|
|
| Passed |
720194365 |
62.54 % |
716371114 |
62.84 % |
3823251 |
0.53 % |
| Filtered |
431399736 |
37.46 % |
423639680 |
37.16 % |
7760056 |
1.08 % |
| |
|
|
|
|
|
|
| q20 |
399327900 |
92.57 % |
397871501 |
93.92 % |
1456399 |
18.77 % |
| q20,qd2 |
14858073 |
3.44 % |
8929317 |
2.11 % |
5928756 |
76.40 % |
| q20,mq40 |
10387592 |
2.41 % |
10312434 |
2.43 % |
75158 |
0.97 % |
| q20,qd2,mq40 |
2847689 |
0.66 % |
2751350 |
0.65 % |
96339 |
1.24 % |
| qd2 |
2656328 |
0.62 % |
2597745 |
0.61 % |
58583 |
0.75 % |
| mq40 |
1270188 |
0.29 % |
1136464 |
0.27 % |
133724 |
1.72 % |
| qd2,mq40 |
50005 |
0.01 % |
40869 |
0.01 % |
9136 |
0.12 % |
| qd2,fs60,mq40 |
787 |
0.00 % |
0 |
0.00 % |
787 |
0.01 % |
| fs60 |
391 |
0.00 % |
0 |
0.00 % |
391 |
0.01 % |
| fs60,mq40 |
309 |
0.00 % |
0 |
0.00 % |
309 |
0.00 % |
| qd2,fs60 |
277 |
0.00 % |
0 |
0.00 % |
277 |
0.00 % |
| q20,qd2,fs60 |
120 |
0.00 % |
0 |
0.00 % |
120 |
0.00 % |
| q20,qd2,fs60,mq40 |
76 |
0.00 % |
0 |
0.00 % |
76 |
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 |
3750355 |
28.21 % |
| Transition |
G>A |
All |
1048449 |
7.89 % |
| Transition |
T>C |
All |
3444504 |
25.91 % |
| Transition |
C>T |
All |
1083751 |
8.15 % |
| Transversion |
A>C |
All |
221080 |
1.66 % |
| Transversion |
C>A |
All |
1159931 |
8.73 % |
| Transversion |
T>G |
All |
236845 |
1.78 % |
| Transversion |
G>T |
All |
1151223 |
8.66 % |
| Transversion |
A>T |
All |
356577 |
2.68 % |
| Transversion |
T>A |
All |
362574 |
2.73 % |
| Transversion |
C>G |
All |
244226 |
1.84 % |
| Transversion |
G>C |
All |
233361 |
1.76 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
474560 |
16.59 % |
| Transition |
G>A |
Passed |
458813 |
16.04 % |
| Transition |
T>C |
Passed |
476085 |
16.65 % |
| Transition |
C>T |
Passed |
466040 |
16.29 % |
| Transversion |
A>C |
Passed |
122118 |
4.27 % |
| Transversion |
C>A |
Passed |
132583 |
4.64 % |
| Transversion |
T>G |
Passed |
122299 |
4.28 % |
| Transversion |
G>T |
Passed |
131493 |
4.60 % |
| Transversion |
A>T |
Passed |
113854 |
3.98 % |
| Transversion |
T>A |
Passed |
114058 |
3.99 % |
| Transversion |
C>G |
Passed |
123731 |
4.33 % |
| Transversion |
G>C |
Passed |
124484 |
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 |
2.35 |
9327059 |
3965817 |
| Passed |
1.90 |
1875498 |
984620 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |