/EXTERNAL CREST/variants/K006438_1_lane_gembs
BACK
SAMPLE K006438_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1214229446 |
741769393 |
61.09 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1214229446 |
100% |
1122899873 |
92.48 % |
91329573 |
7.52 % |
| |
|
|
|
|
|
|
| Passed |
753619260 |
62.07 % |
735337569 |
65.49 % |
18281691 |
2.43 % |
| Filtered |
460610186 |
37.93 % |
387562304 |
34.51 % |
73047882 |
9.69 % |
| |
|
|
|
|
|
|
| q20 |
308317926 |
66.94 % |
290741188 |
75.02 % |
17576738 |
24.06 % |
| q20,qd2 |
74438859 |
16.16 % |
25138917 |
6.49 % |
49299942 |
67.49 % |
| q20,mq40 |
38990298 |
8.46 % |
37413332 |
9.65 % |
1576966 |
2.16 % |
| mq40 |
24864654 |
5.40 % |
23241351 |
6.00 % |
1623303 |
2.22 % |
| qd2 |
7203971 |
1.56 % |
6488681 |
1.67 % |
715290 |
0.98 % |
| q20,qd2,mq40 |
6648887 |
1.44 % |
4421833 |
1.14 % |
2227054 |
3.05 % |
| qd2,mq40 |
145014 |
0.03 % |
117002 |
0.03 % |
28012 |
0.04 % |
| fs60 |
356 |
0.00 % |
0 |
0.00 % |
356 |
0.00 % |
| fs60,mq40 |
156 |
0.00 % |
0 |
0.00 % |
156 |
0.00 % |
| q20,qd2,fs60 |
35 |
0.00 % |
0 |
0.00 % |
35 |
0.00 % |
| q20,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| qd2,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
24603828 |
26.38 % |
| Transition |
G>A |
All |
9075575 |
9.73 % |
| Transition |
T>C |
All |
26091227 |
27.98 % |
| Transition |
C>T |
All |
6171906 |
6.62 % |
| Transversion |
A>C |
All |
1938959 |
2.08 % |
| Transversion |
C>A |
All |
3707514 |
3.98 % |
| Transversion |
T>G |
All |
3354908 |
3.60 % |
| Transversion |
G>T |
All |
3269184 |
3.51 % |
| Transversion |
A>T |
All |
5410610 |
5.80 % |
| Transversion |
T>A |
All |
6206549 |
6.66 % |
| Transversion |
C>G |
All |
2036097 |
2.18 % |
| Transversion |
G>C |
All |
1385491 |
1.49 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1631125 |
22.89 % |
| Transition |
G>A |
Passed |
748547 |
10.51 % |
| Transition |
T>C |
Passed |
2055697 |
28.85 % |
| Transition |
C>T |
Passed |
509560 |
7.15 % |
| Transversion |
A>C |
Passed |
233972 |
3.28 % |
| Transversion |
C>A |
Passed |
295344 |
4.15 % |
| Transversion |
T>G |
Passed |
389105 |
5.46 % |
| Transversion |
G>T |
Passed |
172538 |
2.42 % |
| Transversion |
A>T |
Passed |
192807 |
2.71 % |
| Transversion |
T>A |
Passed |
405703 |
5.69 % |
| Transversion |
C>G |
Passed |
284678 |
4.00 % |
| Transversion |
G>C |
Passed |
205822 |
2.89 % |
| |
|
|
|
|
| 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 |
2.41 |
65942536 |
27309312 |
| Passed |
2.27 |
4944929 |
2179969 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |