/EXTERNAL CREST/variants/K006470_1_lane_gembs
BACK
SAMPLE K006470_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1111034374 |
20980348 |
1.89 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1111034374 |
100% |
1065745421 |
95.92 % |
45288953 |
4.08 % |
| |
|
|
|
|
|
|
| Passed |
39922691 |
3.59 % |
20331071 |
1.91 % |
19591620 |
49.07 % |
| Filtered |
1071111683 |
96.41 % |
1045414350 |
98.09 % |
25697333 |
64.37 % |
| |
|
|
|
|
|
|
| q20 |
901401079 |
84.16 % |
889391747 |
85.08 % |
12009332 |
46.73 % |
| q20,qd2 |
88866892 |
8.30 % |
77505181 |
7.41 % |
11361711 |
44.21 % |
| q20,mq40 |
62725916 |
5.86 % |
62024320 |
5.93 % |
701596 |
2.73 % |
| q20,qd2,mq40 |
16373017 |
1.53 % |
15956485 |
1.53 % |
416532 |
1.62 % |
| mq40 |
1739589 |
0.16 % |
532744 |
0.05 % |
1206845 |
4.70 % |
| qd2,mq40 |
2815 |
0.00 % |
2022 |
0.00 % |
793 |
0.00 % |
| qd2 |
2353 |
0.00 % |
1851 |
0.00 % |
502 |
0.00 % |
| fs60,mq40 |
17 |
0.00 % |
0 |
0.00 % |
17 |
0.00 % |
| fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
7532065 |
15.21 % |
| Transition |
G>A |
All |
3064421 |
6.19 % |
| Transition |
T>C |
All |
7480314 |
15.11 % |
| Transition |
C>T |
All |
2030252 |
4.10 % |
| Transversion |
A>C |
All |
1517063 |
3.06 % |
| Transversion |
C>A |
All |
4450238 |
8.99 % |
| Transversion |
T>G |
All |
3066839 |
6.19 % |
| Transversion |
G>T |
All |
4540427 |
9.17 % |
| Transversion |
A>T |
All |
6216665 |
12.56 % |
| Transversion |
T>A |
All |
6193763 |
12.51 % |
| Transversion |
C>G |
All |
2166908 |
4.38 % |
| Transversion |
G>C |
All |
1252953 |
2.53 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
108967 |
16.57 % |
| Transition |
G>A |
Passed |
71515 |
10.87 % |
| Transition |
T>C |
Passed |
103881 |
15.79 % |
| Transition |
C>T |
Passed |
46791 |
7.11 % |
| Transversion |
A>C |
Passed |
33817 |
5.14 % |
| Transversion |
C>A |
Passed |
43648 |
6.64 % |
| Transversion |
T>G |
Passed |
58261 |
8.86 % |
| Transversion |
G>T |
Passed |
31999 |
4.86 % |
| Transversion |
A>T |
Passed |
27560 |
4.19 % |
| Transversion |
T>A |
Passed |
47867 |
7.28 % |
| Transversion |
C>G |
Passed |
47987 |
7.30 % |
| Transversion |
G>C |
Passed |
35479 |
5.39 % |
| |
|
|
|
|
| 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 |
0.68 |
20107052 |
29404856 |
| Passed |
1.01 |
331154 |
326618 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |