/CEMT/variants/A75622_1_lane_gembs
BACK
SAMPLE A75622_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1178506805 |
1025989809 |
87.06 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1178506805 |
100% |
1158015436 |
98.26 % |
20491369 |
1.74 % |
| |
|
|
|
|
|
|
| Passed |
1028486628 |
87.27 % |
1022209743 |
88.27 % |
6276885 |
0.61 % |
| Filtered |
150020177 |
12.73 % |
135805693 |
11.73 % |
14214484 |
1.38 % |
| |
|
|
|
|
|
|
| q20 |
114836701 |
76.55 % |
113824270 |
83.81 % |
1012431 |
7.12 % |
| q20,qd2 |
16057970 |
10.70 % |
3968404 |
2.92 % |
12089566 |
85.05 % |
| q20,mq40 |
11269594 |
7.51 % |
11135352 |
8.20 % |
134242 |
0.94 % |
| mq40 |
2895012 |
1.93 % |
2606560 |
1.92 % |
288452 |
2.03 % |
| q20,qd2,mq40 |
2635109 |
1.76 % |
2457315 |
1.81 % |
177794 |
1.25 % |
| qd2 |
2263868 |
1.51 % |
1765190 |
1.30 % |
498678 |
3.51 % |
| qd2,mq40 |
60092 |
0.04 % |
48602 |
0.04 % |
11490 |
0.08 % |
| qd2,fs60,mq40 |
799 |
0.00 % |
0 |
0.00 % |
799 |
0.01 % |
| qd2,fs60 |
384 |
0.00 % |
0 |
0.00 % |
384 |
0.00 % |
| fs60,mq40 |
321 |
0.00 % |
0 |
0.00 % |
321 |
0.00 % |
| fs60 |
189 |
0.00 % |
0 |
0.00 % |
189 |
0.00 % |
| q20,qd2,fs60,mq40 |
73 |
0.00 % |
0 |
0.00 % |
73 |
0.00 % |
| q20,qd2,fs60 |
64 |
0.00 % |
0 |
0.00 % |
64 |
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 |
8143469 |
36.87 % |
| Transition |
G>A |
All |
1061722 |
4.81 % |
| Transition |
T>C |
All |
8189415 |
37.08 % |
| Transition |
C>T |
All |
1068895 |
4.84 % |
| Transversion |
A>C |
All |
384655 |
1.74 % |
| Transversion |
C>A |
All |
553943 |
2.51 % |
| Transversion |
T>G |
All |
390043 |
1.77 % |
| Transversion |
G>T |
All |
539677 |
2.44 % |
| Transversion |
A>T |
All |
520226 |
2.36 % |
| Transversion |
T>A |
All |
534926 |
2.42 % |
| Transversion |
C>G |
All |
351605 |
1.59 % |
| Transversion |
G>C |
All |
348796 |
1.58 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1011949 |
20.75 % |
| Transition |
G>A |
Passed |
683050 |
14.00 % |
| Transition |
T>C |
Passed |
958625 |
19.65 % |
| Transition |
C>T |
Passed |
683218 |
14.01 % |
| Transversion |
A>C |
Passed |
200825 |
4.12 % |
| Transversion |
C>A |
Passed |
208719 |
4.28 % |
| Transversion |
T>G |
Passed |
203106 |
4.16 % |
| Transversion |
G>T |
Passed |
197137 |
4.04 % |
| Transversion |
A>T |
Passed |
171479 |
3.52 % |
| Transversion |
T>A |
Passed |
176438 |
3.62 % |
| Transversion |
C>G |
Passed |
191746 |
3.93 % |
| Transversion |
G>C |
Passed |
191013 |
3.92 % |
| |
|
|
|
|
| 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 |
5.09 |
18463501 |
3623871 |
| Passed |
2.17 |
3336842 |
1540463 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |