/cemt/variants/A34408_3_lane_gembs
BACK
SAMPLE A34408_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1159484937 |
624287290 |
53.84 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1159484937 |
100% |
1136272194 |
98.00 % |
23212743 |
2.00 % |
| |
|
|
|
|
|
|
| Passed |
627815695 |
54.15 % |
620866238 |
54.64 % |
6949457 |
1.11 % |
| Filtered |
531669242 |
45.85 % |
515405956 |
45.36 % |
16263286 |
2.59 % |
| |
|
|
|
|
|
|
| q20 |
476180910 |
89.56 % |
471845769 |
91.55 % |
4335141 |
26.66 % |
| q20,qd2 |
27516114 |
5.18 % |
16632081 |
3.23 % |
10884033 |
66.92 % |
| q20,mq40 |
11489420 |
2.16 % |
11294033 |
2.19 % |
195387 |
1.20 % |
| qd2 |
11361955 |
2.14 % |
10920562 |
2.12 % |
441393 |
2.71 % |
| q20,qd2,mq40 |
3376876 |
0.64 % |
3160058 |
0.61 % |
216818 |
1.33 % |
| mq40 |
1669409 |
0.31 % |
1500430 |
0.29 % |
168979 |
1.04 % |
| qd2,mq40 |
63305 |
0.01 % |
53023 |
0.01 % |
10282 |
0.06 % |
| q20,qd2,fs60 |
3385 |
0.00 % |
0 |
0.00 % |
3385 |
0.02 % |
| qd2,fs60 |
2996 |
0.00 % |
0 |
0.00 % |
2996 |
0.02 % |
| fs60 |
2903 |
0.00 % |
0 |
0.00 % |
2903 |
0.02 % |
| qd2,fs60,mq40 |
1448 |
0.00 % |
0 |
0.00 % |
1448 |
0.01 % |
| fs60,mq40 |
330 |
0.00 % |
0 |
0.00 % |
330 |
0.00 % |
| q20,qd2,fs60,mq40 |
182 |
0.00 % |
0 |
0.00 % |
182 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
6555845 |
26.03 % |
| Transition |
G>A |
All |
2472825 |
9.82 % |
| Transition |
T>C |
All |
6250246 |
24.81 % |
| Transition |
C>T |
All |
2453428 |
9.74 % |
| Transversion |
A>C |
All |
501075 |
1.99 % |
| Transversion |
C>A |
All |
1466578 |
5.82 % |
| Transversion |
T>G |
All |
519948 |
2.06 % |
| Transversion |
G>T |
All |
1457366 |
5.79 % |
| Transversion |
A>T |
All |
1321738 |
5.25 % |
| Transversion |
T>A |
All |
1351143 |
5.36 % |
| Transversion |
C>G |
All |
427661 |
1.70 % |
| Transversion |
G>C |
All |
412446 |
1.64 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
647508 |
17.56 % |
| Transition |
G>A |
Passed |
569643 |
15.45 % |
| Transition |
T>C |
Passed |
647285 |
17.55 % |
| Transition |
C>T |
Passed |
573183 |
15.54 % |
| Transversion |
A>C |
Passed |
153465 |
4.16 % |
| Transversion |
C>A |
Passed |
168034 |
4.56 % |
| Transversion |
T>G |
Passed |
153849 |
4.17 % |
| Transversion |
G>T |
Passed |
167531 |
4.54 % |
| Transversion |
A>T |
Passed |
150646 |
4.09 % |
| Transversion |
T>A |
Passed |
150689 |
4.09 % |
| Transversion |
C>G |
Passed |
152530 |
4.14 % |
| Transversion |
G>C |
Passed |
153352 |
4.16 % |
| |
|
|
|
|
| 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 |
2.38 |
17732344 |
7457955 |
| Passed |
1.95 |
2437619 |
1250096 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |