/CEMT/variants/A95334_2_lane_gembs
BACK
SAMPLE A95334_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1167155722 |
1037216986 |
88.87 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1167155722 |
100% |
1153617141 |
98.84 % |
13538581 |
1.16 % |
| |
|
|
|
|
|
|
| Passed |
1038636818 |
88.99 % |
1034253259 |
89.65 % |
4383559 |
0.42 % |
| Filtered |
128518904 |
11.01 % |
119363882 |
10.35 % |
9155022 |
0.88 % |
| |
|
|
|
|
|
|
| q20 |
78916051 |
61.40 % |
78149198 |
65.47 % |
766853 |
8.38 % |
| qd2 |
24776065 |
19.28 % |
24281782 |
20.34 % |
494283 |
5.40 % |
| q20,qd2 |
9889575 |
7.70 % |
2576624 |
2.16 % |
7312951 |
79.88 % |
| q20,mq40 |
9175369 |
7.14 % |
9067842 |
7.60 % |
107527 |
1.17 % |
| mq40 |
3234624 |
2.52 % |
2981513 |
2.50 % |
253111 |
2.76 % |
| q20,qd2,mq40 |
2385963 |
1.86 % |
2222583 |
1.86 % |
163380 |
1.78 % |
| qd2,mq40 |
101285 |
0.08 % |
84340 |
0.07 % |
16945 |
0.19 % |
| fs60 |
15810 |
0.01 % |
0 |
0.00 % |
15810 |
0.17 % |
| qd2,fs60 |
13781 |
0.01 % |
0 |
0.00 % |
13781 |
0.15 % |
| q20,qd2,fs60 |
6375 |
0.00 % |
0 |
0.00 % |
6375 |
0.07 % |
| qd2,fs60,mq40 |
3050 |
0.00 % |
0 |
0.00 % |
3050 |
0.03 % |
| fs60,mq40 |
665 |
0.00 % |
0 |
0.00 % |
665 |
0.01 % |
| q20,qd2,fs60,mq40 |
271 |
0.00 % |
0 |
0.00 % |
271 |
0.00 % |
| q20,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
5432718 |
35.52 % |
| Transition |
G>A |
All |
966981 |
6.32 % |
| Transition |
T>C |
All |
5384996 |
35.21 % |
| Transition |
C>T |
All |
968672 |
6.33 % |
| Transversion |
A>C |
All |
296149 |
1.94 % |
| Transversion |
C>A |
All |
374551 |
2.45 % |
| Transversion |
T>G |
All |
301256 |
1.97 % |
| Transversion |
G>T |
All |
364801 |
2.39 % |
| Transversion |
A>T |
All |
331509 |
2.17 % |
| Transversion |
T>A |
All |
340500 |
2.23 % |
| Transversion |
C>G |
All |
268292 |
1.75 % |
| Transversion |
G>C |
All |
265117 |
1.73 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
801272 |
19.14 % |
| Transition |
G>A |
Passed |
612189 |
14.62 % |
| Transition |
T>C |
Passed |
807616 |
19.29 % |
| Transition |
C>T |
Passed |
613986 |
14.67 % |
| Transversion |
A>C |
Passed |
178790 |
4.27 % |
| Transversion |
C>A |
Passed |
179297 |
4.28 % |
| Transversion |
T>G |
Passed |
179539 |
4.29 % |
| Transversion |
G>T |
Passed |
170497 |
4.07 % |
| Transversion |
A>T |
Passed |
152395 |
3.64 % |
| Transversion |
T>A |
Passed |
154248 |
3.68 % |
| Transversion |
C>G |
Passed |
168240 |
4.02 % |
| Transversion |
G>C |
Passed |
167840 |
4.01 % |
| |
|
|
|
|
| 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 |
5.02 |
12753367 |
2542175 |
| Passed |
2.10 |
2835063 |
1350846 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |