/EXTERNAL CREST/variants/K006448_1_lane_gembs
BACK
SAMPLE K006448_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1187312626 |
550032636 |
46.33 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1187312626 |
100% |
1108656921 |
93.38 % |
78655705 |
6.62 % |
| |
|
|
|
|
|
|
| Passed |
569083949 |
47.93 % |
545835755 |
49.23 % |
23248194 |
4.09 % |
| Filtered |
618228677 |
52.07 % |
562821166 |
50.77 % |
55407511 |
9.74 % |
| |
|
|
|
|
|
|
| q20 |
520160794 |
84.14 % |
501033741 |
89.02 % |
19127053 |
34.52 % |
| q20,qd2 |
65358034 |
10.57 % |
31090215 |
5.52 % |
34267819 |
61.85 % |
| q20,mq40 |
16017861 |
2.59 % |
15554809 |
2.76 % |
463052 |
0.84 % |
| qd2 |
8448349 |
1.37 % |
7972712 |
1.42 % |
475637 |
0.86 % |
| q20,qd2,mq40 |
5871070 |
0.95 % |
5441737 |
0.97 % |
429333 |
0.77 % |
| mq40 |
2328825 |
0.38 % |
1695330 |
0.30 % |
633495 |
1.14 % |
| qd2,mq40 |
41468 |
0.01 % |
32622 |
0.01 % |
8846 |
0.02 % |
| q20,qd2,fs60 |
1397 |
0.00 % |
0 |
0.00 % |
1397 |
0.00 % |
| fs60 |
341 |
0.00 % |
0 |
0.00 % |
341 |
0.00 % |
| fs60,mq40 |
167 |
0.00 % |
0 |
0.00 % |
167 |
0.00 % |
| qd2,fs60,mq40 |
139 |
0.00 % |
0 |
0.00 % |
139 |
0.00 % |
| qd2,fs60 |
122 |
0.00 % |
0 |
0.00 % |
122 |
0.00 % |
| q20,qd2,fs60,mq40 |
98 |
0.00 % |
0 |
0.00 % |
98 |
0.00 % |
| q20,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
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 |
19173914 |
23.40 % |
| Transition |
G>A |
All |
5705699 |
6.96 % |
| Transition |
T>C |
All |
19052507 |
23.25 % |
| Transition |
C>T |
All |
4787014 |
5.84 % |
| Transversion |
A>C |
All |
2628805 |
3.21 % |
| Transversion |
C>A |
All |
4448256 |
5.43 % |
| Transversion |
T>G |
All |
3564845 |
4.35 % |
| Transversion |
G>T |
All |
4241044 |
5.17 % |
| Transversion |
A>T |
All |
6925375 |
8.45 % |
| Transversion |
T>A |
All |
7416520 |
9.05 % |
| Transversion |
C>G |
All |
2201941 |
2.69 % |
| Transversion |
G>C |
All |
1807752 |
2.21 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
978135 |
20.77 % |
| Transition |
G>A |
Passed |
479650 |
10.19 % |
| Transition |
T>C |
Passed |
1184253 |
25.15 % |
| Transition |
C>T |
Passed |
430409 |
9.14 % |
| Transversion |
A>C |
Passed |
216886 |
4.61 % |
| Transversion |
C>A |
Passed |
194474 |
4.13 % |
| Transversion |
T>G |
Passed |
277564 |
5.89 % |
| Transversion |
G>T |
Passed |
154953 |
3.29 % |
| Transversion |
A>T |
Passed |
156586 |
3.33 % |
| Transversion |
T>A |
Passed |
229387 |
4.87 % |
| Transversion |
C>G |
Passed |
220805 |
4.69 % |
| Transversion |
G>C |
Passed |
185607 |
3.94 % |
| |
|
|
|
|
| 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 |
1.47 |
48719134 |
33234538 |
| Passed |
1.88 |
3072447 |
1636262 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |