/EXTERNAL BLUEPRINT/variants/K006293_10_lane_gembs
BACK
SAMPLE K006293_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1137333977 |
726177120 |
63.85 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1137333977 |
100% |
1124755479 |
98.89 % |
12578498 |
1.11 % |
| |
|
|
|
|
|
|
| Passed |
728016798 |
64.01 % |
724640522 |
64.43 % |
3376276 |
0.46 % |
| Filtered |
409317179 |
35.99 % |
400114957 |
35.57 % |
9202222 |
1.26 % |
| |
|
|
|
|
|
|
| q20 |
356055609 |
86.99 % |
354641296 |
88.63 % |
1414313 |
15.37 % |
| q20,qd2 |
29330384 |
7.17 % |
22047217 |
5.51 % |
7283167 |
79.15 % |
| q20,mq40 |
13506067 |
3.30 % |
13415241 |
3.35 % |
90826 |
0.99 % |
| mq40 |
5235035 |
1.28 % |
5075540 |
1.27 % |
159495 |
1.73 % |
| q20,qd2,mq40 |
3058971 |
0.75 % |
2904801 |
0.73 % |
154170 |
1.68 % |
| qd2 |
2062776 |
0.50 % |
1975690 |
0.49 % |
87086 |
0.95 % |
| qd2,mq40 |
64216 |
0.02 % |
55172 |
0.01 % |
9044 |
0.10 % |
| q20,qd2,fs60 |
980 |
0.00 % |
0 |
0.00 % |
980 |
0.01 % |
| qd2,fs60,mq40 |
945 |
0.00 % |
0 |
0.00 % |
945 |
0.01 % |
| fs60 |
764 |
0.00 % |
0 |
0.00 % |
764 |
0.01 % |
| qd2,fs60 |
645 |
0.00 % |
0 |
0.00 % |
645 |
0.01 % |
| q20,qd2,fs60,mq40 |
396 |
0.00 % |
0 |
0.00 % |
396 |
0.00 % |
| fs60,mq40 |
386 |
0.00 % |
0 |
0.00 % |
386 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3399957 |
23.48 % |
| Transition |
G>A |
All |
2594791 |
17.92 % |
| Transition |
T>C |
All |
3314666 |
22.89 % |
| Transition |
C>T |
All |
2506454 |
17.31 % |
| Transversion |
A>C |
All |
206324 |
1.42 % |
| Transversion |
C>A |
All |
548293 |
3.79 % |
| Transversion |
T>G |
All |
214064 |
1.48 % |
| Transversion |
G>T |
All |
543854 |
3.76 % |
| Transversion |
A>T |
All |
392406 |
2.71 % |
| Transversion |
T>A |
All |
382020 |
2.64 % |
| Transversion |
C>G |
All |
190644 |
1.32 % |
| Transversion |
G>C |
All |
185944 |
1.28 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
416847 |
18.18 % |
| Transition |
G>A |
Passed |
388169 |
16.93 % |
| Transition |
T>C |
Passed |
416602 |
18.17 % |
| Transition |
C>T |
Passed |
388962 |
16.97 % |
| Transversion |
A>C |
Passed |
89018 |
3.88 % |
| Transversion |
C>A |
Passed |
85596 |
3.73 % |
| Transversion |
T>G |
Passed |
89289 |
3.89 % |
| Transversion |
G>T |
Passed |
85639 |
3.74 % |
| Transversion |
A>T |
Passed |
62626 |
2.73 % |
| Transversion |
T>A |
Passed |
62459 |
2.72 % |
| Transversion |
C>G |
Passed |
103327 |
4.51 % |
| Transversion |
G>C |
Passed |
104079 |
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 |
4.44 |
11815868 |
2663549 |
| Passed |
2.36 |
1610580 |
682033 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |