/EXTERNAL CREST/variants/K006443_1_lane_gembs
BACK
SAMPLE K006443_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1192903689 |
543243443 |
45.54 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1192903689 |
100% |
1111566339 |
93.18 % |
81337350 |
6.82 % |
| |
|
|
|
|
|
|
| Passed |
563207166 |
47.21 % |
538891790 |
48.48 % |
24315376 |
4.32 % |
| Filtered |
629696523 |
52.79 % |
572674549 |
51.52 % |
57021974 |
10.12 % |
| |
|
|
|
|
|
|
| q20 |
524655128 |
83.32 % |
505349830 |
88.24 % |
19305298 |
33.86 % |
| q20,qd2 |
69654339 |
11.06 % |
34173023 |
5.97 % |
35481316 |
62.22 % |
| q20,mq40 |
17042435 |
2.71 % |
16536848 |
2.89 % |
505587 |
0.89 % |
| qd2 |
9448560 |
1.50 % |
8897499 |
1.55 % |
551061 |
0.97 % |
| q20,qd2,mq40 |
6268542 |
1.00 % |
5786649 |
1.01 % |
481893 |
0.85 % |
| mq40 |
2577131 |
0.41 % |
1892727 |
0.33 % |
684404 |
1.20 % |
| qd2,mq40 |
47751 |
0.01 % |
37973 |
0.01 % |
9778 |
0.02 % |
| q20,qd2,fs60 |
1570 |
0.00 % |
0 |
0.00 % |
1570 |
0.00 % |
| fs60 |
410 |
0.00 % |
0 |
0.00 % |
410 |
0.00 % |
| qd2,fs60 |
209 |
0.00 % |
0 |
0.00 % |
209 |
0.00 % |
| qd2,fs60,mq40 |
175 |
0.00 % |
0 |
0.00 % |
175 |
0.00 % |
| fs60,mq40 |
151 |
0.00 % |
0 |
0.00 % |
151 |
0.00 % |
| q20,qd2,fs60,mq40 |
117 |
0.00 % |
0 |
0.00 % |
117 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
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 |
18413182 |
21.70 % |
| Transition |
G>A |
All |
6226373 |
7.34 % |
| Transition |
T>C |
All |
21053047 |
24.81 % |
| Transition |
C>T |
All |
4728069 |
5.57 % |
| Transversion |
A>C |
All |
2657160 |
3.13 % |
| Transversion |
C>A |
All |
4767031 |
5.62 % |
| Transversion |
T>G |
All |
3681151 |
4.34 % |
| Transversion |
G>T |
All |
4321998 |
5.09 % |
| Transversion |
A>T |
All |
6968004 |
8.21 % |
| Transversion |
T>A |
All |
7925980 |
9.34 % |
| Transversion |
C>G |
All |
2271274 |
2.68 % |
| Transversion |
G>C |
All |
1827379 |
2.15 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
894074 |
18.49 % |
| Transition |
G>A |
Passed |
504371 |
10.43 % |
| Transition |
T>C |
Passed |
1300959 |
26.90 % |
| Transition |
C>T |
Passed |
413246 |
8.54 % |
| Transversion |
A>C |
Passed |
209219 |
4.33 % |
| Transversion |
C>A |
Passed |
229924 |
4.75 % |
| Transversion |
T>G |
Passed |
290687 |
6.01 % |
| Transversion |
G>T |
Passed |
149628 |
3.09 % |
| Transversion |
A>T |
Passed |
149052 |
3.08 % |
| Transversion |
T>A |
Passed |
282225 |
5.84 % |
| Transversion |
C>G |
Passed |
229733 |
4.75 % |
| Transversion |
G>C |
Passed |
183596 |
3.80 % |
| |
|
|
|
|
| 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 |
1.46 |
50420671 |
34419977 |
| Passed |
1.81 |
3112650 |
1724064 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |