/EXTERNAL BLUEPRINT/variants/K006350_12_lane_gembs
BACK
SAMPLE K006350_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1110529498 |
624175921 |
56.21 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1110529498 |
100% |
1095460213 |
98.64 % |
15069285 |
1.36 % |
| |
|
|
|
|
|
|
| Passed |
626196086 |
56.39 % |
622829404 |
56.86 % |
3366682 |
0.54 % |
| Filtered |
484333412 |
43.61 % |
472630809 |
43.14 % |
11702603 |
1.87 % |
| |
|
|
|
|
|
|
| q20 |
414024741 |
85.48 % |
412470246 |
87.27 % |
1554495 |
13.28 % |
| q20,qd2 |
43952890 |
9.07 % |
34393570 |
7.28 % |
9559320 |
81.69 % |
| q20,mq40 |
14867261 |
3.07 % |
14757347 |
3.12 % |
109914 |
0.94 % |
| mq40 |
5758944 |
1.19 % |
5585865 |
1.18 % |
173079 |
1.48 % |
| q20,qd2,mq40 |
3330543 |
0.69 % |
3124024 |
0.66 % |
206519 |
1.76 % |
| qd2 |
2322791 |
0.48 % |
2238815 |
0.47 % |
83976 |
0.72 % |
| qd2,mq40 |
71055 |
0.01 % |
60942 |
0.01 % |
10113 |
0.09 % |
| q20,qd2,fs60 |
1577 |
0.00 % |
0 |
0.00 % |
1577 |
0.01 % |
| fs60 |
1077 |
0.00 % |
0 |
0.00 % |
1077 |
0.01 % |
| qd2,fs60,mq40 |
951 |
0.00 % |
0 |
0.00 % |
951 |
0.01 % |
| qd2,fs60 |
634 |
0.00 % |
0 |
0.00 % |
634 |
0.01 % |
| fs60,mq40 |
475 |
0.00 % |
0 |
0.00 % |
475 |
0.00 % |
| q20,qd2,fs60,mq40 |
469 |
0.00 % |
0 |
0.00 % |
469 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
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 |
3505952 |
20.30 % |
| Transition |
G>A |
All |
3715840 |
21.52 % |
| Transition |
T>C |
All |
3371539 |
19.52 % |
| Transition |
C>T |
All |
3609747 |
20.90 % |
| Transversion |
A>C |
All |
214024 |
1.24 % |
| Transversion |
C>A |
All |
672825 |
3.90 % |
| Transversion |
T>G |
All |
224761 |
1.30 % |
| Transversion |
G>T |
All |
671491 |
3.89 % |
| Transversion |
A>T |
All |
457756 |
2.65 % |
| Transversion |
T>A |
All |
450285 |
2.61 % |
| Transversion |
C>G |
All |
190898 |
1.11 % |
| Transversion |
G>C |
All |
184717 |
1.07 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
371815 |
18.84 % |
| Transition |
G>A |
Passed |
336248 |
17.04 % |
| Transition |
T>C |
Passed |
369528 |
18.73 % |
| Transition |
C>T |
Passed |
335801 |
17.02 % |
| Transversion |
A>C |
Passed |
74603 |
3.78 % |
| Transversion |
C>A |
Passed |
68479 |
3.47 % |
| Transversion |
T>G |
Passed |
74480 |
3.77 % |
| Transversion |
G>T |
Passed |
68982 |
3.50 % |
| Transversion |
A>T |
Passed |
47018 |
2.38 % |
| Transversion |
T>A |
Passed |
47032 |
2.38 % |
| Transversion |
C>G |
Passed |
89495 |
4.54 % |
| Transversion |
G>C |
Passed |
89634 |
4.54 % |
| |
|
|
|
|
| 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 |
4.63 |
14203078 |
3066757 |
| Passed |
2.53 |
1413392 |
559723 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |