/EXTERNAL CREST/variants/K006449_1_lane_gembs
BACK
SAMPLE K006449_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1215647133 |
784951239 |
64.57 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1215647133 |
100% |
1118956733 |
92.05 % |
96690400 |
7.95 % |
| |
|
|
|
|
|
|
| Passed |
797649306 |
65.62 % |
775262395 |
69.28 % |
22386911 |
2.81 % |
| Filtered |
417997827 |
34.38 % |
343694338 |
30.72 % |
74303489 |
9.32 % |
| |
|
|
|
|
|
|
| q20 |
260985699 |
62.44 % |
244089341 |
71.02 % |
16896358 |
22.74 % |
| q20,qd2 |
78256648 |
18.72 % |
27420764 |
7.98 % |
50835884 |
68.42 % |
| q20,mq40 |
29278538 |
7.00 % |
27904885 |
8.12 % |
1373653 |
1.85 % |
| mq40 |
23443012 |
5.61 % |
21935627 |
6.38 % |
1507385 |
2.03 % |
| qd2 |
19221364 |
4.60 % |
17592708 |
5.12 % |
1628656 |
2.19 % |
| q20,qd2,mq40 |
6463020 |
1.55 % |
4468794 |
1.30 % |
1994226 |
2.68 % |
| qd2,mq40 |
339011 |
0.08 % |
282219 |
0.08 % |
56792 |
0.08 % |
| fs60 |
8435 |
0.00 % |
0 |
0.00 % |
8435 |
0.01 % |
| fs60,mq40 |
1325 |
0.00 % |
0 |
0.00 % |
1325 |
0.00 % |
| qd2,fs60 |
311 |
0.00 % |
0 |
0.00 % |
311 |
0.00 % |
| q20,qd2,fs60 |
298 |
0.00 % |
0 |
0.00 % |
298 |
0.00 % |
| q20,fs60 |
106 |
0.00 % |
0 |
0.00 % |
106 |
0.00 % |
| qd2,fs60,mq40 |
27 |
0.00 % |
0 |
0.00 % |
27 |
0.00 % |
| q20,qd2,fs60,mq40 |
27 |
0.00 % |
0 |
0.00 % |
27 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
21488743 |
21.77 % |
| Transition |
G>A |
All |
8484239 |
8.59 % |
| Transition |
T>C |
All |
30358636 |
30.75 % |
| Transition |
C>T |
All |
7626716 |
7.72 % |
| Transversion |
A>C |
All |
2631060 |
2.66 % |
| Transversion |
C>A |
All |
3997887 |
4.05 % |
| Transversion |
T>G |
All |
3690521 |
3.74 % |
| Transversion |
G>T |
All |
3733405 |
3.78 % |
| Transversion |
A>T |
All |
6411298 |
6.49 % |
| Transversion |
T>A |
All |
6771946 |
6.86 % |
| Transversion |
C>G |
All |
2058054 |
2.08 % |
| Transversion |
G>C |
All |
1477433 |
1.50 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1994999 |
19.26 % |
| Transition |
G>A |
Passed |
919844 |
8.88 % |
| Transition |
T>C |
Passed |
3433857 |
33.15 % |
| Transition |
C>T |
Passed |
646018 |
6.24 % |
| Transversion |
A>C |
Passed |
532758 |
5.14 % |
| Transversion |
C>A |
Passed |
400303 |
3.86 % |
| Transversion |
T>G |
Passed |
685753 |
6.62 % |
| Transversion |
G>T |
Passed |
207793 |
2.01 % |
| Transversion |
A>T |
Passed |
257429 |
2.48 % |
| Transversion |
T>A |
Passed |
571110 |
5.51 % |
| Transversion |
C>G |
Passed |
408243 |
3.94 % |
| Transversion |
G>C |
Passed |
301773 |
2.91 % |
| |
|
|
|
|
| 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 |
2.21 |
67958334 |
30771604 |
| Passed |
2.08 |
6994718 |
3365162 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |