/EXTERNAL CREST/variants/K006435_1_lane_gembs
BACK
SAMPLE K006435_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1227654442 |
653018909 |
53.19 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1227654442 |
100% |
1114956799 |
90.82 % |
112697643 |
9.18 % |
| |
|
|
|
|
|
|
| Passed |
670295350 |
54.60 % |
645791704 |
57.92 % |
24503646 |
3.66 % |
| Filtered |
557359092 |
45.40 % |
469165095 |
42.08 % |
88193997 |
13.16 % |
| |
|
|
|
|
|
|
| q20 |
392217670 |
70.37 % |
368994650 |
78.65 % |
23223020 |
26.33 % |
| q20,qd2 |
86706536 |
15.56 % |
28311797 |
6.03 % |
58394739 |
66.21 % |
| q20,mq40 |
43936315 |
7.88 % |
42176407 |
8.99 % |
1759908 |
2.00 % |
| mq40 |
21017417 |
3.77 % |
19133206 |
4.08 % |
1884211 |
2.14 % |
| q20,qd2,mq40 |
7296638 |
1.31 % |
5000715 |
1.07 % |
2295923 |
2.60 % |
| qd2 |
6089173 |
1.09 % |
5471681 |
1.17 % |
617492 |
0.70 % |
| qd2,mq40 |
94518 |
0.02 % |
76639 |
0.02 % |
17879 |
0.02 % |
| fs60 |
472 |
0.00 % |
0 |
0.00 % |
472 |
0.00 % |
| fs60,mq40 |
276 |
0.00 % |
0 |
0.00 % |
276 |
0.00 % |
| q20,qd2,fs60 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| q20,fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| qd2,fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| q20,qd2,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| qd2,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
26693727 |
23.27 % |
| Transition |
G>A |
All |
10045095 |
8.76 % |
| Transition |
T>C |
All |
31942829 |
27.84 % |
| Transition |
C>T |
All |
6913635 |
6.03 % |
| Transversion |
A>C |
All |
2863862 |
2.50 % |
| Transversion |
C>A |
All |
5281103 |
4.60 % |
| Transversion |
T>G |
All |
4522398 |
3.94 % |
| Transversion |
G>T |
All |
4938631 |
4.30 % |
| Transversion |
A>T |
All |
8149957 |
7.10 % |
| Transversion |
T>A |
All |
8634055 |
7.53 % |
| Transversion |
C>G |
All |
2792900 |
2.43 % |
| Transversion |
G>C |
All |
1955266 |
1.70 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1601659 |
20.59 % |
| Transition |
G>A |
Passed |
715250 |
9.20 % |
| Transition |
T>C |
Passed |
2462235 |
31.66 % |
| Transition |
C>T |
Passed |
452973 |
5.82 % |
| Transversion |
A>C |
Passed |
278268 |
3.58 % |
| Transversion |
C>A |
Passed |
342595 |
4.41 % |
| Transversion |
T>G |
Passed |
456018 |
5.86 % |
| Transversion |
G>T |
Passed |
190935 |
2.46 % |
| Transversion |
A>T |
Passed |
226906 |
2.92 % |
| Transversion |
T>A |
Passed |
484349 |
6.23 % |
| Transversion |
C>G |
Passed |
329450 |
4.24 % |
| Transversion |
G>C |
Passed |
236671 |
3.04 % |
| |
|
|
|
|
| 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 |
1.93 |
75595286 |
39138172 |
| Passed |
2.06 |
5232117 |
2545192 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |