/EXTERNAL BLUEPRINT/variants/K006320_8_lane_gembs
BACK
SAMPLE K006320_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1107977178 |
260542450 |
23.52 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1107977178 |
100% |
1082664115 |
97.72 % |
25313063 |
2.28 % |
| |
|
|
|
|
|
|
| Passed |
267776938 |
24.17 % |
259413845 |
23.96 % |
8363093 |
3.12 % |
| Filtered |
840200240 |
75.83 % |
823250270 |
76.04 % |
16949970 |
6.33 % |
| |
|
|
|
|
|
|
| q20 |
762641965 |
90.77 % |
756323400 |
91.87 % |
6318565 |
37.28 % |
| q20,qd2 |
60548657 |
7.21 % |
50175130 |
6.09 % |
10373527 |
61.20 % |
| q20,mq40 |
11374931 |
1.35 % |
11293636 |
1.37 % |
81295 |
0.48 % |
| q20,qd2,mq40 |
5129851 |
0.61 % |
5071489 |
0.62 % |
58362 |
0.34 % |
| mq40 |
333757 |
0.04 % |
234508 |
0.03 % |
99249 |
0.59 % |
| qd2 |
155893 |
0.02 % |
139799 |
0.02 % |
16094 |
0.09 % |
| qd2,mq40 |
14797 |
0.00 % |
12308 |
0.00 % |
2489 |
0.01 % |
| qd2,fs60,mq40 |
198 |
0.00 % |
0 |
0.00 % |
198 |
0.00 % |
| fs60,mq40 |
63 |
0.00 % |
0 |
0.00 % |
63 |
0.00 % |
| qd2,fs60 |
60 |
0.00 % |
0 |
0.00 % |
60 |
0.00 % |
| q20,qd2,fs60,mq40 |
49 |
0.00 % |
0 |
0.00 % |
49 |
0.00 % |
| fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
8759589 |
32.07 % |
| Transition |
G>A |
All |
1233557 |
4.52 % |
| Transition |
T>C |
All |
8810550 |
32.25 % |
| Transition |
C>T |
All |
1237276 |
4.53 % |
| Transversion |
A>C |
All |
412034 |
1.51 % |
| Transversion |
C>A |
All |
1335245 |
4.89 % |
| Transversion |
T>G |
All |
410633 |
1.50 % |
| Transversion |
G>T |
All |
1325357 |
4.85 % |
| Transversion |
A>T |
All |
1583322 |
5.80 % |
| Transversion |
T>A |
All |
1590933 |
5.82 % |
| Transversion |
C>G |
All |
308154 |
1.13 % |
| Transversion |
G>C |
All |
310251 |
1.14 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
273294 |
19.31 % |
| Transition |
G>A |
Passed |
206616 |
14.60 % |
| Transition |
T>C |
Passed |
271869 |
19.21 % |
| Transition |
C>T |
Passed |
207665 |
14.67 % |
| Transversion |
A>C |
Passed |
57036 |
4.03 % |
| Transversion |
C>A |
Passed |
61227 |
4.33 % |
| Transversion |
T>G |
Passed |
57107 |
4.04 % |
| Transversion |
G>T |
Passed |
60337 |
4.26 % |
| Transversion |
A>T |
Passed |
56381 |
3.98 % |
| Transversion |
T>A |
Passed |
57091 |
4.03 % |
| Transversion |
C>G |
Passed |
53602 |
3.79 % |
| Transversion |
G>C |
Passed |
53034 |
3.75 % |
| |
|
|
|
|
| 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 |
2.75 |
20040972 |
7275929 |
| Passed |
2.10 |
959444 |
455815 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |