/EXTERNAL BLUEPRINT/variants/K010500_1_lane_gembs
BACK
SAMPLE K010500_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1110841769 |
626938291 |
56.44 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1110841769 |
100% |
1093011937 |
98.39 % |
17829832 |
1.61 % |
| |
|
|
|
|
|
|
| Passed |
628740271 |
56.60 % |
625638376 |
57.24 % |
3101895 |
0.49 % |
| Filtered |
482101498 |
43.40 % |
467373561 |
42.76 % |
14727937 |
2.34 % |
| |
|
|
|
|
|
|
| q20 |
403776658 |
83.75 % |
402066154 |
86.03 % |
1710504 |
11.61 % |
| q20,qd2 |
50980268 |
10.57 % |
38568088 |
8.25 % |
12412180 |
84.28 % |
| q20,mq40 |
15138073 |
3.14 % |
15026811 |
3.22 % |
111262 |
0.76 % |
| mq40 |
6658651 |
1.38 % |
6488344 |
1.39 % |
170307 |
1.16 % |
| q20,qd2,mq40 |
3397266 |
0.70 % |
3191714 |
0.68 % |
205552 |
1.40 % |
| qd2 |
2053560 |
0.43 % |
1955858 |
0.42 % |
97702 |
0.66 % |
| qd2,mq40 |
88786 |
0.02 % |
76592 |
0.02 % |
12194 |
0.08 % |
| q20,qd2,fs60 |
2489 |
0.00 % |
0 |
0.00 % |
2489 |
0.02 % |
| fs60 |
1817 |
0.00 % |
0 |
0.00 % |
1817 |
0.01 % |
| qd2,fs60 |
1369 |
0.00 % |
0 |
0.00 % |
1369 |
0.01 % |
| qd2,fs60,mq40 |
1333 |
0.00 % |
0 |
0.00 % |
1333 |
0.01 % |
| q20,qd2,fs60,mq40 |
635 |
0.00 % |
0 |
0.00 % |
635 |
0.00 % |
| fs60,mq40 |
590 |
0.00 % |
0 |
0.00 % |
590 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3353362 |
15.02 % |
| Transition |
G>A |
All |
6564448 |
29.41 % |
| Transition |
T>C |
All |
3134101 |
14.04 % |
| Transition |
C>T |
All |
6383368 |
28.60 % |
| Transversion |
A>C |
All |
215558 |
0.97 % |
| Transversion |
C>A |
All |
581140 |
2.60 % |
| Transversion |
T>G |
All |
234007 |
1.05 % |
| Transversion |
G>T |
All |
574594 |
2.57 % |
| Transversion |
A>T |
All |
449917 |
2.02 % |
| Transversion |
T>A |
All |
446020 |
2.00 % |
| Transversion |
C>G |
All |
197387 |
0.88 % |
| Transversion |
G>C |
All |
185661 |
0.83 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
372495 |
19.17 % |
| Transition |
G>A |
Passed |
328247 |
16.90 % |
| Transition |
T>C |
Passed |
372986 |
19.20 % |
| Transition |
C>T |
Passed |
329007 |
16.94 % |
| Transversion |
A>C |
Passed |
72116 |
3.71 % |
| Transversion |
C>A |
Passed |
65784 |
3.39 % |
| Transversion |
T>G |
Passed |
72079 |
3.71 % |
| Transversion |
G>T |
Passed |
65962 |
3.40 % |
| Transversion |
A>T |
Passed |
44757 |
2.30 % |
| Transversion |
T>A |
Passed |
44883 |
2.31 % |
| Transversion |
C>G |
Passed |
87224 |
4.49 % |
| Transversion |
G>C |
Passed |
87093 |
4.48 % |
| |
|
|
|
|
| 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 |
6.74 |
19435279 |
2884284 |
| Passed |
2.60 |
1402735 |
539898 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |