/EXTERNAL DEEP/variants/K006107_K006108_2_lane_gembs
BACK
SAMPLE K006107_K006108_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1184379677 |
453847991 |
38.32 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1184379677 |
100% |
1117110372 |
94.32 % |
67269305 |
5.68 % |
| |
|
|
|
|
|
|
| Passed |
465185944 |
39.28 % |
448062509 |
40.11 % |
17123435 |
3.68 % |
| Filtered |
719193733 |
60.72 % |
669047863 |
59.89 % |
50145870 |
10.78 % |
| |
|
|
|
|
|
|
| q20 |
641580110 |
89.21 % |
623120500 |
93.14 % |
18459610 |
36.81 % |
| q20,qd2 |
55434336 |
7.71 % |
24933199 |
3.73 % |
30501137 |
60.82 % |
| q20,mq40 |
14282870 |
1.99 % |
13902492 |
2.08 % |
380378 |
0.76 % |
| q20,qd2,mq40 |
4276995 |
0.59 % |
4023656 |
0.60 % |
253339 |
0.51 % |
| qd2 |
2433838 |
0.34 % |
2243018 |
0.34 % |
190820 |
0.38 % |
| mq40 |
1163288 |
0.16 % |
807588 |
0.12 % |
355700 |
0.71 % |
| qd2,mq40 |
21967 |
0.00 % |
17410 |
0.00 % |
4557 |
0.01 % |
| qd2,fs60,mq40 |
134 |
0.00 % |
0 |
0.00 % |
134 |
0.00 % |
| fs60,mq40 |
87 |
0.00 % |
0 |
0.00 % |
87 |
0.00 % |
| qd2,fs60 |
47 |
0.00 % |
0 |
0.00 % |
47 |
0.00 % |
| fs60 |
44 |
0.00 % |
0 |
0.00 % |
44 |
0.00 % |
| q20,qd2,fs60,mq40 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| q20,qd2,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
16633513 |
24.17 % |
| Transition |
G>A |
All |
4585101 |
6.66 % |
| Transition |
T>C |
All |
19130899 |
27.80 % |
| Transition |
C>T |
All |
2741645 |
3.98 % |
| Transversion |
A>C |
All |
3367695 |
4.89 % |
| Transversion |
C>A |
All |
4984300 |
7.24 % |
| Transversion |
T>G |
All |
3922101 |
5.70 % |
| Transversion |
G>T |
All |
4582510 |
6.66 % |
| Transversion |
A>T |
All |
1890923 |
2.75 % |
| Transversion |
T>A |
All |
2415163 |
3.51 % |
| Transversion |
C>G |
All |
2359235 |
3.43 % |
| Transversion |
G>C |
All |
2200724 |
3.20 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1035298 |
17.42 % |
| Transition |
G>A |
Passed |
627386 |
10.56 % |
| Transition |
T>C |
Passed |
1923232 |
32.36 % |
| Transition |
C>T |
Passed |
441754 |
7.43 % |
| Transversion |
A>C |
Passed |
216612 |
3.64 % |
| Transversion |
C>A |
Passed |
336410 |
5.66 % |
| Transversion |
T>G |
Passed |
273926 |
4.61 % |
| Transversion |
G>T |
Passed |
257621 |
4.33 % |
| Transversion |
A>T |
Passed |
139423 |
2.35 % |
| Transversion |
T>A |
Passed |
229097 |
3.85 % |
| Transversion |
C>G |
Passed |
235989 |
3.97 % |
| Transversion |
G>C |
Passed |
226570 |
3.81 % |
| |
|
|
|
|
| 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 |
1.68 |
43091158 |
25722651 |
| Passed |
2.10 |
4027670 |
1915648 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |