/cemt/variants/A54777_3_lane_gembs
BACK
SAMPLE A54777_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1161313927 |
661424017 |
56.95 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1161313927 |
100% |
1139253452 |
98.10 % |
22060475 |
1.90 % |
| |
|
|
|
|
|
|
| Passed |
664970065 |
57.26 % |
659176483 |
57.86 % |
5793582 |
0.87 % |
| Filtered |
496343862 |
42.74 % |
480076969 |
42.14 % |
16266893 |
2.45 % |
| |
|
|
|
|
|
|
| q20 |
444902491 |
89.64 % |
440420092 |
91.74 % |
4482399 |
27.56 % |
| q20,qd2 |
24476894 |
4.93 % |
13501153 |
2.81 % |
10975741 |
67.47 % |
| q20,mq40 |
11191914 |
2.25 % |
10998718 |
2.29 % |
193196 |
1.19 % |
| qd2 |
10697914 |
2.16 % |
10481046 |
2.18 % |
216868 |
1.33 % |
| q20,qd2,mq40 |
3298818 |
0.66 % |
3093526 |
0.64 % |
205292 |
1.26 % |
| mq40 |
1695173 |
0.34 % |
1524527 |
0.32 % |
170646 |
1.05 % |
| qd2,mq40 |
69210 |
0.01 % |
57907 |
0.01 % |
11303 |
0.07 % |
| q20,qd2,fs60 |
3670 |
0.00 % |
0 |
0.00 % |
3670 |
0.02 % |
| qd2,fs60 |
2867 |
0.00 % |
0 |
0.00 % |
2867 |
0.02 % |
| fs60 |
2713 |
0.00 % |
0 |
0.00 % |
2713 |
0.02 % |
| qd2,fs60,mq40 |
1570 |
0.00 % |
0 |
0.00 % |
1570 |
0.01 % |
| fs60,mq40 |
409 |
0.00 % |
0 |
0.00 % |
409 |
0.00 % |
| q20,qd2,fs60,mq40 |
210 |
0.00 % |
0 |
0.00 % |
210 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
7657089 |
31.14 % |
| Transition |
G>A |
All |
1992527 |
8.10 % |
| Transition |
T>C |
All |
6386950 |
25.98 % |
| Transition |
C>T |
All |
2068260 |
8.41 % |
| Transversion |
A>C |
All |
455154 |
1.85 % |
| Transversion |
C>A |
All |
1168829 |
4.75 % |
| Transversion |
T>G |
All |
528354 |
2.15 % |
| Transversion |
G>T |
All |
1118225 |
4.55 % |
| Transversion |
A>T |
All |
1152612 |
4.69 % |
| Transversion |
T>A |
All |
1212707 |
4.93 % |
| Transversion |
C>G |
All |
452668 |
1.84 % |
| Transversion |
G>C |
All |
392675 |
1.60 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
574043 |
19.01 % |
| Transition |
G>A |
Passed |
453018 |
15.00 % |
| Transition |
T>C |
Passed |
535192 |
17.72 % |
| Transition |
C>T |
Passed |
458205 |
15.17 % |
| Transversion |
A>C |
Passed |
124663 |
4.13 % |
| Transversion |
C>A |
Passed |
135404 |
4.48 % |
| Transversion |
T>G |
Passed |
127546 |
4.22 % |
| Transversion |
G>T |
Passed |
134550 |
4.46 % |
| Transversion |
A>T |
Passed |
121355 |
4.02 % |
| Transversion |
T>A |
Passed |
123216 |
4.08 % |
| Transversion |
C>G |
Passed |
116417 |
3.86 % |
| Transversion |
G>C |
Passed |
116103 |
3.84 % |
| |
|
|
|
|
| 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 |
2.79 |
18104826 |
6481224 |
| Passed |
2.02 |
2020458 |
999254 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |