/EXTERNAL CREST/variants/K006455_1_lane_gembs
BACK
SAMPLE K006455_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1223253606 |
709506648 |
58.00 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1223253606 |
100% |
1111956536 |
90.90 % |
111297070 |
9.10 % |
| |
|
|
|
|
|
|
| Passed |
726349349 |
59.38 % |
701847648 |
63.12 % |
24501701 |
3.37 % |
| Filtered |
496904257 |
40.62 % |
410108888 |
36.88 % |
86795369 |
11.95 % |
| |
|
|
|
|
|
|
| q20 |
327195023 |
65.85 % |
307034457 |
74.87 % |
20160566 |
23.23 % |
| q20,qd2 |
88258132 |
17.76 % |
28603579 |
6.97 % |
59654553 |
68.73 % |
| q20,mq40 |
40499516 |
8.15 % |
38884349 |
9.48 % |
1615167 |
1.86 % |
| mq40 |
23286766 |
4.69 % |
21335315 |
5.20 % |
1951451 |
2.25 % |
| qd2 |
10230543 |
2.06 % |
9254563 |
2.26 % |
975980 |
1.12 % |
| q20,qd2,mq40 |
7303180 |
1.47 % |
4889400 |
1.19 % |
2413780 |
2.78 % |
| qd2,mq40 |
130309 |
0.03 % |
107225 |
0.03 % |
23084 |
0.03 % |
| fs60 |
449 |
0.00 % |
0 |
0.00 % |
449 |
0.00 % |
| fs60,mq40 |
262 |
0.00 % |
0 |
0.00 % |
262 |
0.00 % |
| q20,qd2,fs60 |
53 |
0.00 % |
0 |
0.00 % |
53 |
0.00 % |
| q20,fs60 |
20 |
0.00 % |
0 |
0.00 % |
20 |
0.00 % |
| qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
28728179 |
25.34 % |
| Transition |
G>A |
All |
9875114 |
8.71 % |
| Transition |
T>C |
All |
33459591 |
29.52 % |
| Transition |
C>T |
All |
6771546 |
5.97 % |
| Transversion |
A>C |
All |
2228712 |
1.97 % |
| Transversion |
C>A |
All |
4961533 |
4.38 % |
| Transversion |
T>G |
All |
3584996 |
3.16 % |
| Transversion |
G>T |
All |
4679563 |
4.13 % |
| Transversion |
A>T |
All |
7292011 |
6.43 % |
| Transversion |
T>A |
All |
7670644 |
6.77 % |
| Transversion |
C>G |
All |
2389523 |
2.11 % |
| Transversion |
G>C |
All |
1707973 |
1.51 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1866285 |
22.52 % |
| Transition |
G>A |
Passed |
774495 |
9.34 % |
| Transition |
T>C |
Passed |
2660632 |
32.10 % |
| Transition |
C>T |
Passed |
495579 |
5.98 % |
| Transversion |
A>C |
Passed |
262661 |
3.17 % |
| Transversion |
C>A |
Passed |
350034 |
4.22 % |
| Transversion |
T>G |
Passed |
423193 |
5.11 % |
| Transversion |
G>T |
Passed |
194456 |
2.35 % |
| Transversion |
A>T |
Passed |
223605 |
2.70 % |
| Transversion |
T>A |
Passed |
469371 |
5.66 % |
| Transversion |
C>G |
Passed |
328203 |
3.96 % |
| Transversion |
G>C |
Passed |
239755 |
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 |
2.28 |
78834430 |
34514955 |
| Passed |
2.33 |
5796991 |
2491278 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |