/EXTERNAL CREST/variants/K006464_1_lane_gembs
BACK
SAMPLE K006464_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1204935423 |
589916142 |
48.96 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1204935423 |
100% |
1110433894 |
92.16 % |
94501529 |
7.84 % |
| |
|
|
|
|
|
|
| Passed |
610066746 |
50.63 % |
582968798 |
52.50 % |
27097948 |
4.44 % |
| Filtered |
594868677 |
49.37 % |
527465096 |
47.50 % |
67403581 |
11.05 % |
| |
|
|
|
|
|
|
| q20 |
487634789 |
81.97 % |
464486005 |
88.06 % |
23148784 |
34.34 % |
| q20,qd2 |
69240565 |
11.64 % |
27824004 |
5.28 % |
41416561 |
61.45 % |
| q20,mq40 |
17484969 |
2.94 % |
16866943 |
3.20 % |
618026 |
0.92 % |
| qd2 |
11876676 |
2.00 % |
11017196 |
2.09 % |
859480 |
1.28 % |
| q20,qd2,mq40 |
6116358 |
1.03 % |
5545072 |
1.05 % |
571286 |
0.85 % |
| mq40 |
2455840 |
0.41 % |
1684287 |
0.32 % |
771553 |
1.14 % |
| qd2,mq40 |
52427 |
0.01 % |
41589 |
0.01 % |
10838 |
0.02 % |
| q20,qd2,fs60 |
4387 |
0.00 % |
0 |
0.00 % |
4387 |
0.01 % |
| fs60 |
1687 |
0.00 % |
0 |
0.00 % |
1687 |
0.00 % |
| qd2,fs60 |
369 |
0.00 % |
0 |
0.00 % |
369 |
0.00 % |
| qd2,fs60,mq40 |
239 |
0.00 % |
0 |
0.00 % |
239 |
0.00 % |
| q20,qd2,fs60,mq40 |
176 |
0.00 % |
0 |
0.00 % |
176 |
0.00 % |
| fs60,mq40 |
174 |
0.00 % |
0 |
0.00 % |
174 |
0.00 % |
| q20,fs60 |
21 |
0.00 % |
0 |
0.00 % |
21 |
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 |
23563094 |
24.20 % |
| Transition |
G>A |
All |
7333018 |
7.53 % |
| Transition |
T>C |
All |
22481084 |
23.09 % |
| Transition |
C>T |
All |
6377096 |
6.55 % |
| Transversion |
A>C |
All |
2941037 |
3.02 % |
| Transversion |
C>A |
All |
5100467 |
5.24 % |
| Transversion |
T>G |
All |
4066953 |
4.18 % |
| Transversion |
G>T |
All |
4854389 |
4.99 % |
| Transversion |
A>T |
All |
7726858 |
7.94 % |
| Transversion |
T>A |
All |
8361208 |
8.59 % |
| Transversion |
C>G |
All |
2559308 |
2.63 % |
| Transversion |
G>C |
All |
2009421 |
2.06 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1432039 |
19.84 % |
| Transition |
G>A |
Passed |
724399 |
10.03 % |
| Transition |
T>C |
Passed |
1634323 |
22.64 % |
| Transition |
C>T |
Passed |
684945 |
9.49 % |
| Transversion |
A>C |
Passed |
383765 |
5.32 % |
| Transversion |
C>A |
Passed |
315734 |
4.37 % |
| Transversion |
T>G |
Passed |
421989 |
5.84 % |
| Transversion |
G>T |
Passed |
299013 |
4.14 % |
| Transversion |
A>T |
Passed |
301486 |
4.18 % |
| Transversion |
T>A |
Passed |
375319 |
5.20 % |
| Transversion |
C>G |
Passed |
337689 |
4.68 % |
| Transversion |
G>C |
Passed |
309043 |
4.28 % |
| |
|
|
|
|
| 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 |
1.59 |
59754292 |
37619641 |
| Passed |
1.63 |
4475706 |
2744038 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |