/cemt/variants/A59695_3_lane_gembs
BACK
SAMPLE A59695_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1160164004 |
1022285195 |
88.12 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1160164004 |
100% |
1146713451 |
98.84 % |
13450553 |
1.16 % |
| |
|
|
|
|
|
|
| Passed |
1023165134 |
88.19 % |
1019351391 |
88.89 % |
3813743 |
0.37 % |
| Filtered |
136998870 |
11.81 % |
127362060 |
11.11 % |
9636810 |
0.94 % |
| |
|
|
|
|
|
|
| q20 |
100063437 |
73.04 % |
98687071 |
77.49 % |
1376366 |
14.28 % |
| q20,qd2 |
13204913 |
9.64 % |
6049421 |
4.75 % |
7155492 |
74.25 % |
| q20,mq40 |
11923692 |
8.70 % |
11670115 |
9.16 % |
253577 |
2.63 % |
| qd2 |
5559361 |
4.06 % |
5273178 |
4.14 % |
286183 |
2.97 % |
| q20,qd2,mq40 |
3233722 |
2.36 % |
2923737 |
2.30 % |
309985 |
3.22 % |
| mq40 |
2948205 |
2.15 % |
2706823 |
2.13 % |
241382 |
2.50 % |
| qd2,mq40 |
62623 |
0.05 % |
51715 |
0.04 % |
10908 |
0.11 % |
| qd2,fs60,mq40 |
926 |
0.00 % |
0 |
0.00 % |
926 |
0.01 % |
| fs60 |
546 |
0.00 % |
0 |
0.00 % |
546 |
0.01 % |
| q20,qd2,fs60 |
532 |
0.00 % |
0 |
0.00 % |
532 |
0.01 % |
| qd2,fs60 |
489 |
0.00 % |
0 |
0.00 % |
489 |
0.01 % |
| fs60,mq40 |
338 |
0.00 % |
0 |
0.00 % |
338 |
0.00 % |
| q20,qd2,fs60,mq40 |
82 |
0.00 % |
0 |
0.00 % |
82 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
4003668 |
26.29 % |
| Transition |
G>A |
All |
1169115 |
7.68 % |
| Transition |
T>C |
All |
4001542 |
26.28 % |
| Transition |
C>T |
All |
1169257 |
7.68 % |
| Transversion |
A>C |
All |
414417 |
2.72 % |
| Transversion |
C>A |
All |
835822 |
5.49 % |
| Transversion |
T>G |
All |
412297 |
2.71 % |
| Transversion |
G>T |
All |
854735 |
5.61 % |
| Transversion |
A>T |
All |
870768 |
5.72 % |
| Transversion |
T>A |
All |
846551 |
5.56 % |
| Transversion |
C>G |
All |
323036 |
2.12 % |
| Transversion |
G>C |
All |
325585 |
2.14 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
697899 |
16.94 % |
| Transition |
G>A |
Passed |
628130 |
15.25 % |
| Transition |
T>C |
Passed |
702146 |
17.04 % |
| Transition |
C>T |
Passed |
629260 |
15.27 % |
| Transversion |
A>C |
Passed |
189059 |
4.59 % |
| Transversion |
C>A |
Passed |
202038 |
4.90 % |
| Transversion |
T>G |
Passed |
188248 |
4.57 % |
| Transversion |
G>T |
Passed |
199235 |
4.84 % |
| Transversion |
A>T |
Passed |
178356 |
4.33 % |
| Transversion |
T>A |
Passed |
179191 |
4.35 % |
| Transversion |
C>G |
Passed |
162589 |
3.95 % |
| Transversion |
G>C |
Passed |
163540 |
3.97 % |
| |
|
|
|
|
| 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 |
2.12 |
10343582 |
4883211 |
| Passed |
1.82 |
2657435 |
1462256 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |