/EXTERNAL CREST/variants/K006472_1_lane_gembs
BACK
SAMPLE K006472_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1139737518 |
59283715 |
5.20 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1139737518 |
100% |
1080460701 |
94.80 % |
59276817 |
5.20 % |
| |
|
|
|
|
|
|
| Passed |
80869905 |
7.10 % |
58232997 |
5.39 % |
22636908 |
27.99 % |
| Filtered |
1058867613 |
92.90 % |
1022227704 |
94.61 % |
36639909 |
45.31 % |
| |
|
|
|
|
|
|
| q20 |
905152337 |
85.48 % |
889584554 |
87.02 % |
15567783 |
42.49 % |
| q20,qd2 |
71054164 |
6.71 % |
52937944 |
5.18 % |
18116220 |
49.44 % |
| q20,mq40 |
65959661 |
6.23 % |
65065944 |
6.37 % |
893717 |
2.44 % |
| q20,qd2,mq40 |
13950070 |
1.32 % |
13347251 |
1.31 % |
602819 |
1.65 % |
| mq40 |
2740679 |
0.26 % |
1283587 |
0.13 % |
1457092 |
3.98 % |
| qd2 |
6590 |
0.00 % |
5455 |
0.00 % |
1135 |
0.00 % |
| qd2,mq40 |
4076 |
0.00 % |
2969 |
0.00 % |
1107 |
0.00 % |
| fs60,mq40 |
27 |
0.00 % |
0 |
0.00 % |
27 |
0.00 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
9723246 |
15.42 % |
| Transition |
G>A |
All |
4101004 |
6.50 % |
| Transition |
T>C |
All |
9383118 |
14.88 % |
| Transition |
C>T |
All |
2501583 |
3.97 % |
| Transversion |
A>C |
All |
1850638 |
2.93 % |
| Transversion |
C>A |
All |
5556970 |
8.81 % |
| Transversion |
T>G |
All |
3887438 |
6.16 % |
| Transversion |
G>T |
All |
5866495 |
9.30 % |
| Transversion |
A>T |
All |
8168811 |
12.95 % |
| Transversion |
T>A |
All |
7815033 |
12.39 % |
| Transversion |
C>G |
All |
2725767 |
4.32 % |
| Transversion |
G>C |
All |
1489197 |
2.36 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
190967 |
17.70 % |
| Transition |
G>A |
Passed |
121284 |
11.24 % |
| Transition |
T>C |
Passed |
181690 |
16.84 % |
| Transition |
C>T |
Passed |
73795 |
6.84 % |
| Transversion |
A>C |
Passed |
51728 |
4.79 % |
| Transversion |
C>A |
Passed |
69460 |
6.44 % |
| Transversion |
T>G |
Passed |
92656 |
8.59 % |
| Transversion |
G>T |
Passed |
46989 |
4.35 % |
| Transversion |
A>T |
Passed |
42890 |
3.98 % |
| Transversion |
T>A |
Passed |
80750 |
7.48 % |
| Transversion |
C>G |
Passed |
74676 |
6.92 % |
| Transversion |
G>C |
Passed |
52106 |
4.83 % |
| |
|
|
|
|
| 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 |
0.69 |
25708951 |
37360349 |
| Passed |
1.11 |
567736 |
511255 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |