/EXTERNAL CREST/variants/K006466_K006467_2_lane_gembs
BACK
SAMPLE K006466_K006467_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1202781421 |
630656920 |
52.43 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1202781421 |
100% |
1114680688 |
92.68 % |
88100733 |
7.32 % |
| |
|
|
|
|
|
|
| Passed |
648934429 |
53.95 % |
625212534 |
56.09 % |
23721895 |
3.66 % |
| Filtered |
553846992 |
46.05 % |
489468154 |
43.91 % |
64378838 |
9.92 % |
| |
|
|
|
|
|
|
| q20 |
436107137 |
78.74 % |
416158414 |
85.02 % |
19948723 |
30.99 % |
| q20,qd2 |
67714612 |
12.23 % |
26976416 |
5.51 % |
40738196 |
63.28 % |
| q20,mq40 |
24068386 |
4.35 % |
23205940 |
4.74 % |
862446 |
1.34 % |
| qd2 |
12418747 |
2.24 % |
11674341 |
2.39 % |
744406 |
1.16 % |
| mq40 |
6818558 |
1.23 % |
5745684 |
1.17 % |
1072874 |
1.67 % |
| q20,qd2,mq40 |
6626198 |
1.20 % |
5632978 |
1.15 % |
993220 |
1.54 % |
| qd2,mq40 |
91889 |
0.02 % |
74381 |
0.02 % |
17508 |
0.03 % |
| q20,qd2,fs60 |
882 |
0.00 % |
0 |
0.00 % |
882 |
0.00 % |
| fs60 |
256 |
0.00 % |
0 |
0.00 % |
256 |
0.00 % |
| fs60,mq40 |
110 |
0.00 % |
0 |
0.00 % |
110 |
0.00 % |
| qd2,fs60,mq40 |
95 |
0.00 % |
0 |
0.00 % |
95 |
0.00 % |
| qd2,fs60 |
73 |
0.00 % |
0 |
0.00 % |
73 |
0.00 % |
| q20,qd2,fs60,mq40 |
38 |
0.00 % |
0 |
0.00 % |
38 |
0.00 % |
| q20,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
20547881 |
22.57 % |
| Transition |
G>A |
All |
7079054 |
7.78 % |
| Transition |
T>C |
All |
21756866 |
23.90 % |
| Transition |
C>T |
All |
5707183 |
6.27 % |
| Transversion |
A>C |
All |
2883269 |
3.17 % |
| Transversion |
C>A |
All |
4666029 |
5.13 % |
| Transversion |
T>G |
All |
4028645 |
4.43 % |
| Transversion |
G>T |
All |
4496387 |
4.94 % |
| Transversion |
A>T |
All |
7670621 |
8.43 % |
| Transversion |
T>A |
All |
8152075 |
8.96 % |
| Transversion |
C>G |
All |
2271710 |
2.50 % |
| Transversion |
G>C |
All |
1762774 |
1.94 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1230510 |
20.86 % |
| Transition |
G>A |
Passed |
579810 |
9.83 % |
| Transition |
T>C |
Passed |
1491702 |
25.29 % |
| Transition |
C>T |
Passed |
490780 |
8.32 % |
| Transversion |
A>C |
Passed |
280840 |
4.76 % |
| Transversion |
C>A |
Passed |
241967 |
4.10 % |
| Transversion |
T>G |
Passed |
403514 |
6.84 % |
| Transversion |
G>T |
Passed |
180942 |
3.07 % |
| Transversion |
A>T |
Passed |
197090 |
3.34 % |
| Transversion |
T>A |
Passed |
315764 |
5.35 % |
| Transversion |
C>G |
Passed |
274083 |
4.65 % |
| Transversion |
G>C |
Passed |
210733 |
3.57 % |
| |
|
|
|
|
| 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 |
1.53 |
55090984 |
35931510 |
| Passed |
1.80 |
3792802 |
2104933 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |