/EXTERNAL BLUEPRINT/variants/K006287_14_lane_gembs
BACK
SAMPLE K006287_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1128123959 |
658786193 |
58.40 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1128123959 |
100% |
1115688802 |
98.90 % |
12435157 |
1.10 % |
| |
|
|
|
|
|
|
| Passed |
661081472 |
58.60 % |
657329162 |
58.92 % |
3752310 |
0.57 % |
| Filtered |
467042487 |
41.40 % |
458359640 |
41.08 % |
8682847 |
1.31 % |
| |
|
|
|
|
|
|
| q20 |
417194316 |
89.33 % |
415513917 |
90.65 % |
1680399 |
19.35 % |
| q20,qd2 |
24945429 |
5.34 % |
18495899 |
4.04 % |
6449530 |
74.28 % |
| q20,mq40 |
13992188 |
3.00 % |
13899748 |
3.03 % |
92440 |
1.06 % |
| mq40 |
6298739 |
1.35 % |
6120669 |
1.34 % |
178070 |
2.05 % |
| q20,qd2,mq40 |
2728412 |
0.58 % |
2571948 |
0.56 % |
156464 |
1.80 % |
| qd2 |
1799797 |
0.39 % |
1692006 |
0.37 % |
107791 |
1.24 % |
| qd2,mq40 |
77613 |
0.02 % |
65453 |
0.01 % |
12160 |
0.14 % |
| qd2,fs60,mq40 |
1365 |
0.00 % |
0 |
0.00 % |
1365 |
0.02 % |
| q20,qd2,fs60 |
1345 |
0.00 % |
0 |
0.00 % |
1345 |
0.02 % |
| fs60 |
1268 |
0.00 % |
0 |
0.00 % |
1268 |
0.01 % |
| qd2,fs60 |
1142 |
0.00 % |
0 |
0.00 % |
1142 |
0.01 % |
| fs60,mq40 |
561 |
0.00 % |
0 |
0.00 % |
561 |
0.01 % |
| q20,qd2,fs60,mq40 |
306 |
0.00 % |
0 |
0.00 % |
306 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
3805010 |
25.75 % |
| Transition |
G>A |
All |
2340879 |
15.84 % |
| Transition |
T>C |
All |
3678478 |
24.90 % |
| Transition |
C>T |
All |
2308978 |
15.63 % |
| Transversion |
A>C |
All |
207974 |
1.41 % |
| Transversion |
C>A |
All |
544576 |
3.69 % |
| Transversion |
T>G |
All |
216778 |
1.47 % |
| Transversion |
G>T |
All |
531613 |
3.60 % |
| Transversion |
A>T |
All |
375928 |
2.54 % |
| Transversion |
T>A |
All |
368246 |
2.49 % |
| Transversion |
C>G |
All |
201720 |
1.37 % |
| Transversion |
G>C |
All |
195257 |
1.32 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
391892 |
18.54 % |
| Transition |
G>A |
Passed |
350276 |
16.57 % |
| Transition |
T>C |
Passed |
391736 |
18.54 % |
| Transition |
C>T |
Passed |
350373 |
16.58 % |
| Transversion |
A>C |
Passed |
82937 |
3.92 % |
| Transversion |
C>A |
Passed |
77855 |
3.68 % |
| Transversion |
T>G |
Passed |
82575 |
3.91 % |
| Transversion |
G>T |
Passed |
77262 |
3.66 % |
| Transversion |
A>T |
Passed |
55183 |
2.61 % |
| Transversion |
T>A |
Passed |
54720 |
2.59 % |
| Transversion |
C>G |
Passed |
99161 |
4.69 % |
| Transversion |
G>C |
Passed |
99330 |
4.70 % |
| |
|
|
|
|
| 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 |
4.59 |
12133345 |
2642092 |
| Passed |
2.36 |
1484277 |
629023 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |