/EXTERNAL CREST/variants/K006445_1_lane_gembs
BACK
SAMPLE K006445_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1191509820 |
561849653 |
47.15 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1191509820 |
100% |
1112310391 |
93.35 % |
79199429 |
6.65 % |
| |
|
|
|
|
|
|
| Passed |
581079973 |
48.77 % |
557253431 |
50.10 % |
23826542 |
4.10 % |
| Filtered |
610429847 |
51.23 % |
555056960 |
49.90 % |
55372887 |
9.53 % |
| |
|
|
|
|
|
|
| q20 |
507525990 |
83.14 % |
488991541 |
88.10 % |
18534449 |
33.47 % |
| q20,qd2 |
67913575 |
11.13 % |
33290591 |
6.00 % |
34622984 |
62.53 % |
| q20,mq40 |
16218231 |
2.66 % |
15740970 |
2.84 % |
477261 |
0.86 % |
| qd2 |
10016711 |
1.64 % |
9398345 |
1.69 % |
618366 |
1.12 % |
| q20,qd2,mq40 |
5957307 |
0.98 % |
5491517 |
0.99 % |
465790 |
0.84 % |
| mq40 |
2745956 |
0.45 % |
2104414 |
0.38 % |
641542 |
1.16 % |
| qd2,mq40 |
49379 |
0.01 % |
39582 |
0.01 % |
9797 |
0.02 % |
| q20,qd2,fs60 |
1743 |
0.00 % |
0 |
0.00 % |
1743 |
0.00 % |
| fs60 |
383 |
0.00 % |
0 |
0.00 % |
383 |
0.00 % |
| qd2,fs60 |
184 |
0.00 % |
0 |
0.00 % |
184 |
0.00 % |
| qd2,fs60,mq40 |
144 |
0.00 % |
0 |
0.00 % |
144 |
0.00 % |
| fs60,mq40 |
128 |
0.00 % |
0 |
0.00 % |
128 |
0.00 % |
| q20,qd2,fs60,mq40 |
98 |
0.00 % |
0 |
0.00 % |
98 |
0.00 % |
| q20,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
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 |
17701751 |
21.49 % |
| Transition |
G>A |
All |
6226766 |
7.56 % |
| Transition |
T>C |
All |
20531363 |
24.93 % |
| Transition |
C>T |
All |
4714887 |
5.72 % |
| Transversion |
A>C |
All |
2544437 |
3.09 % |
| Transversion |
C>A |
All |
4580847 |
5.56 % |
| Transversion |
T>G |
All |
3517755 |
4.27 % |
| Transversion |
G>T |
All |
4169034 |
5.06 % |
| Transversion |
A>T |
All |
6804732 |
8.26 % |
| Transversion |
T>A |
All |
7679038 |
9.32 % |
| Transversion |
C>G |
All |
2159250 |
2.62 % |
| Transversion |
G>C |
All |
1728807 |
2.10 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
898611 |
18.16 % |
| Transition |
G>A |
Passed |
541483 |
10.94 % |
| Transition |
T>C |
Passed |
1303830 |
26.35 % |
| Transition |
C>T |
Passed |
447000 |
9.03 % |
| Transversion |
A>C |
Passed |
214352 |
4.33 % |
| Transversion |
C>A |
Passed |
234144 |
4.73 % |
| Transversion |
T>G |
Passed |
291690 |
5.90 % |
| Transversion |
G>T |
Passed |
156468 |
3.16 % |
| Transversion |
A>T |
Passed |
153557 |
3.10 % |
| Transversion |
T>A |
Passed |
281892 |
5.70 % |
| Transversion |
C>G |
Passed |
236094 |
4.77 % |
| Transversion |
G>C |
Passed |
188878 |
3.82 % |
| |
|
|
|
|
| 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 |
1.48 |
49174767 |
33183900 |
| Passed |
1.82 |
3190924 |
1757075 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |