/EXTERNAL CREST/variants/K006450_1_lane_gembs
BACK
SAMPLE K006450_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1217048251 |
771278805 |
63.37 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1217048251 |
100% |
1119263356 |
91.97 % |
97784895 |
8.03 % |
| |
|
|
|
|
|
|
| Passed |
784362823 |
64.45 % |
761682064 |
68.05 % |
22680759 |
2.89 % |
| Filtered |
432685428 |
35.55 % |
357581292 |
31.95 % |
75104136 |
9.58 % |
| |
|
|
|
|
|
|
| q20 |
278619255 |
64.39 % |
260792389 |
72.93 % |
17826866 |
23.74 % |
| q20,qd2 |
77909522 |
18.01 % |
26934792 |
7.53 % |
50974730 |
67.87 % |
| q20,mq40 |
30088000 |
6.95 % |
28737264 |
8.04 % |
1350736 |
1.80 % |
| mq40 |
21520735 |
4.97 % |
20044513 |
5.61 % |
1476222 |
1.97 % |
| qd2 |
18052640 |
4.17 % |
16556379 |
4.63 % |
1496261 |
1.99 % |
| q20,qd2,mq40 |
6237923 |
1.44 % |
4307313 |
1.20 % |
1930610 |
2.57 % |
| qd2,mq40 |
250624 |
0.06 % |
208642 |
0.06 % |
41982 |
0.06 % |
| fs60 |
5286 |
0.00 % |
0 |
0.00 % |
5286 |
0.01 % |
| fs60,mq40 |
924 |
0.00 % |
0 |
0.00 % |
924 |
0.00 % |
| q20,qd2,fs60 |
218 |
0.00 % |
0 |
0.00 % |
218 |
0.00 % |
| qd2,fs60 |
151 |
0.00 % |
0 |
0.00 % |
151 |
0.00 % |
| q20,fs60 |
94 |
0.00 % |
0 |
0.00 % |
94 |
0.00 % |
| q20,qd2,fs60,mq40 |
30 |
0.00 % |
0 |
0.00 % |
30 |
0.00 % |
| qd2,fs60,mq40 |
22 |
0.00 % |
0 |
0.00 % |
22 |
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 |
22640796 |
22.68 % |
| Transition |
G>A |
All |
8605591 |
8.62 % |
| Transition |
T>C |
All |
30609749 |
30.66 % |
| Transition |
C>T |
All |
7254538 |
7.27 % |
| Transversion |
A>C |
All |
2550906 |
2.55 % |
| Transversion |
C>A |
All |
3976375 |
3.98 % |
| Transversion |
T>G |
All |
3647550 |
3.65 % |
| Transversion |
G>T |
All |
3698415 |
3.70 % |
| Transversion |
A>T |
All |
6407921 |
6.42 % |
| Transversion |
T>A |
All |
6757049 |
6.77 % |
| Transversion |
C>G |
All |
2111490 |
2.11 % |
| Transversion |
G>C |
All |
1581727 |
1.58 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2078734 |
20.25 % |
| Transition |
G>A |
Passed |
893379 |
8.70 % |
| Transition |
T>C |
Passed |
3495061 |
34.04 % |
| Transition |
C>T |
Passed |
623321 |
6.07 % |
| Transversion |
A>C |
Passed |
466356 |
4.54 % |
| Transversion |
C>A |
Passed |
379211 |
3.69 % |
| Transversion |
T>G |
Passed |
607777 |
5.92 % |
| Transversion |
G>T |
Passed |
204642 |
1.99 % |
| Transversion |
A>T |
Passed |
254772 |
2.48 % |
| Transversion |
T>A |
Passed |
540094 |
5.26 % |
| Transversion |
C>G |
Passed |
398575 |
3.88 % |
| Transversion |
G>C |
Passed |
325683 |
3.17 % |
| |
|
|
|
|
| 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 |
2.25 |
69110674 |
30731433 |
| Passed |
2.23 |
7090495 |
3177110 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |