/EXTERNAL BLUEPRINT/variants/K006277_11_lane_gembs
BACK
SAMPLE K006277_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1154998620 |
918101490 |
79.49 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1154998620 |
100% |
1139846502 |
98.69 % |
15152118 |
1.31 % |
| |
|
|
|
|
|
|
| Passed |
920187295 |
79.67 % |
915111536 |
80.28 % |
5075759 |
0.55 % |
| Filtered |
234811325 |
20.33 % |
224734966 |
19.72 % |
10076359 |
1.10 % |
| |
|
|
|
|
|
|
| q20 |
192388341 |
81.93 % |
191144816 |
85.05 % |
1243525 |
12.34 % |
| q20,qd2 |
18437627 |
7.85 % |
10525623 |
4.68 % |
7912004 |
78.52 % |
| q20,mq40 |
12272273 |
5.23 % |
12168575 |
5.41 % |
103698 |
1.03 % |
| mq40 |
6349540 |
2.70 % |
6112519 |
2.72 % |
237021 |
2.35 % |
| q20,qd2,mq40 |
2811509 |
1.20 % |
2619607 |
1.17 % |
191902 |
1.90 % |
| qd2 |
2458782 |
1.05 % |
2091332 |
0.93 % |
367450 |
3.65 % |
| qd2,mq40 |
87130 |
0.04 % |
72494 |
0.03 % |
14636 |
0.15 % |
| q20,qd2,fs60 |
1821 |
0.00 % |
0 |
0.00 % |
1821 |
0.02 % |
| qd2,fs60,mq40 |
1415 |
0.00 % |
0 |
0.00 % |
1415 |
0.01 % |
| fs60 |
1244 |
0.00 % |
0 |
0.00 % |
1244 |
0.01 % |
| qd2,fs60 |
768 |
0.00 % |
0 |
0.00 % |
768 |
0.01 % |
| fs60,mq40 |
496 |
0.00 % |
0 |
0.00 % |
496 |
0.00 % |
| q20,qd2,fs60,mq40 |
377 |
0.00 % |
0 |
0.00 % |
377 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
4221165 |
25.36 % |
| Transition |
G>A |
All |
2780272 |
16.70 % |
| Transition |
T>C |
All |
4182135 |
25.12 % |
| Transition |
C>T |
All |
2773828 |
16.66 % |
| Transversion |
A>C |
All |
241533 |
1.45 % |
| Transversion |
C>A |
All |
484774 |
2.91 % |
| Transversion |
T>G |
All |
246639 |
1.48 % |
| Transversion |
G>T |
All |
481851 |
2.89 % |
| Transversion |
A>T |
All |
385046 |
2.31 % |
| Transversion |
T>A |
All |
374649 |
2.25 % |
| Transversion |
C>G |
All |
239198 |
1.44 % |
| Transversion |
G>C |
All |
234781 |
1.41 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
630376 |
18.08 % |
| Transition |
G>A |
Passed |
575642 |
16.51 % |
| Transition |
T>C |
Passed |
614364 |
17.62 % |
| Transition |
C>T |
Passed |
574806 |
16.48 % |
| Transversion |
A>C |
Passed |
139503 |
4.00 % |
| Transversion |
C>A |
Passed |
141813 |
4.07 % |
| Transversion |
T>G |
Passed |
139099 |
3.99 % |
| Transversion |
G>T |
Passed |
141117 |
4.05 % |
| Transversion |
A>T |
Passed |
109413 |
3.14 % |
| Transversion |
T>A |
Passed |
109523 |
3.14 % |
| Transversion |
C>G |
Passed |
155440 |
4.46 % |
| Transversion |
G>C |
Passed |
155990 |
4.47 % |
| |
|
|
|
|
| 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 |
5.19 |
13957400 |
2688471 |
| Passed |
2.19 |
2395188 |
1091898 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |