/EXTERNAL CREST/variants/K006446_1_lane_gembs
BACK
SAMPLE K006446_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1188822982 |
528243799 |
44.43 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1188822982 |
100% |
1108737542 |
93.26 % |
80085440 |
6.74 % |
| |
|
|
|
|
|
|
| Passed |
548140633 |
46.11 % |
523744597 |
47.24 % |
24396036 |
4.45 % |
| Filtered |
640682349 |
53.89 % |
584992945 |
52.76 % |
55689404 |
10.16 % |
| |
|
|
|
|
|
|
| q20 |
534963264 |
83.50 % |
515589231 |
88.14 % |
19374033 |
34.79 % |
| q20,qd2 |
69570679 |
10.86 % |
35478129 |
6.06 % |
34092550 |
61.22 % |
| q20,mq40 |
17256360 |
2.69 % |
16768497 |
2.87 % |
487863 |
0.88 % |
| qd2 |
9777829 |
1.53 % |
9203841 |
1.57 % |
573988 |
1.03 % |
| q20,qd2,mq40 |
6455598 |
1.01 % |
5987882 |
1.02 % |
467716 |
0.84 % |
| mq40 |
2604458 |
0.41 % |
1925580 |
0.33 % |
678878 |
1.22 % |
| qd2,mq40 |
49894 |
0.01 % |
39785 |
0.01 % |
10109 |
0.02 % |
| q20,qd2,fs60 |
2709 |
0.00 % |
0 |
0.00 % |
2709 |
0.00 % |
| fs60 |
707 |
0.00 % |
0 |
0.00 % |
707 |
0.00 % |
| qd2,fs60 |
287 |
0.00 % |
0 |
0.00 % |
287 |
0.00 % |
| qd2,fs60,mq40 |
199 |
0.00 % |
0 |
0.00 % |
199 |
0.00 % |
| fs60,mq40 |
187 |
0.00 % |
0 |
0.00 % |
187 |
0.00 % |
| q20,qd2,fs60,mq40 |
164 |
0.00 % |
0 |
0.00 % |
164 |
0.00 % |
| q20,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
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 |
17501014 |
20.90 % |
| Transition |
G>A |
All |
6353398 |
7.59 % |
| Transition |
T>C |
All |
20737533 |
24.76 % |
| Transition |
C>T |
All |
4897615 |
5.85 % |
| Transversion |
A>C |
All |
2742061 |
3.27 % |
| Transversion |
C>A |
All |
4752222 |
5.68 % |
| Transversion |
T>G |
All |
3551718 |
4.24 % |
| Transversion |
G>T |
All |
4366945 |
5.21 % |
| Transversion |
A>T |
All |
6935423 |
8.28 % |
| Transversion |
T>A |
All |
7749361 |
9.25 % |
| Transversion |
C>G |
All |
2258642 |
2.70 % |
| Transversion |
G>C |
All |
1892234 |
2.26 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
842827 |
17.02 % |
| Transition |
G>A |
Passed |
517555 |
10.45 % |
| Transition |
T>C |
Passed |
1330950 |
26.88 % |
| Transition |
C>T |
Passed |
433926 |
8.76 % |
| Transversion |
A>C |
Passed |
242913 |
4.91 % |
| Transversion |
C>A |
Passed |
242830 |
4.90 % |
| Transversion |
T>G |
Passed |
276891 |
5.59 % |
| Transversion |
G>T |
Passed |
173713 |
3.51 % |
| Transversion |
A>T |
Passed |
171692 |
3.47 % |
| Transversion |
T>A |
Passed |
287922 |
5.82 % |
| Transversion |
C>G |
Passed |
227799 |
4.60 % |
| Transversion |
G>C |
Passed |
201765 |
4.08 % |
| |
|
|
|
|
| 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 |
1.45 |
49489560 |
34248606 |
| Passed |
1.71 |
3125258 |
1825525 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |