/EXTERNAL BLUEPRINT/variants/K006331_15_lane_gembs
BACK
SAMPLE K006331_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1086914181 |
561038481 |
51.62 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1086914181 |
100% |
1068777120 |
98.33 % |
18137061 |
1.67 % |
| |
|
|
|
|
|
|
| Passed |
562716489 |
51.77 % |
559899734 |
52.39 % |
2816755 |
0.50 % |
| Filtered |
524197692 |
48.23 % |
508877386 |
47.61 % |
15320306 |
2.72 % |
| |
|
|
|
|
|
|
| q20 |
430612113 |
82.15 % |
428834466 |
84.27 % |
1777647 |
11.60 % |
| q20,qd2 |
61142402 |
11.66 % |
48184574 |
9.47 % |
12957828 |
84.58 % |
| q20,mq40 |
15636805 |
2.98 % |
15530499 |
3.05 % |
106306 |
0.69 % |
| mq40 |
7072190 |
1.35 % |
6912911 |
1.36 % |
159279 |
1.04 % |
| qd2 |
6052824 |
1.15 % |
5953907 |
1.17 % |
98917 |
0.65 % |
| q20,qd2,mq40 |
3568040 |
0.68 % |
3374361 |
0.66 % |
193679 |
1.26 % |
| qd2,mq40 |
99386 |
0.02 % |
86668 |
0.02 % |
12718 |
0.08 % |
| q20,qd2,fs60 |
4503 |
0.00 % |
0 |
0.00 % |
4503 |
0.03 % |
| qd2,fs60 |
3153 |
0.00 % |
0 |
0.00 % |
3153 |
0.02 % |
| fs60 |
2701 |
0.00 % |
0 |
0.00 % |
2701 |
0.02 % |
| qd2,fs60,mq40 |
1981 |
0.00 % |
0 |
0.00 % |
1981 |
0.01 % |
| q20,qd2,fs60,mq40 |
925 |
0.00 % |
0 |
0.00 % |
925 |
0.01 % |
| fs60,mq40 |
665 |
0.00 % |
0 |
0.00 % |
665 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3133230 |
11.18 % |
| Transition |
G>A |
All |
9729501 |
34.70 % |
| Transition |
T>C |
All |
2882445 |
10.28 % |
| Transition |
C>T |
All |
9557697 |
34.09 % |
| Transversion |
A>C |
All |
206371 |
0.74 % |
| Transversion |
C>A |
All |
545334 |
1.95 % |
| Transversion |
T>G |
All |
227600 |
0.81 % |
| Transversion |
G>T |
All |
535698 |
1.91 % |
| Transversion |
A>T |
All |
422796 |
1.51 % |
| Transversion |
T>A |
All |
425662 |
1.52 % |
| Transversion |
C>G |
All |
191000 |
0.68 % |
| Transversion |
G>C |
All |
179443 |
0.64 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
329480 |
19.54 % |
| Transition |
G>A |
Passed |
287085 |
17.02 % |
| Transition |
T>C |
Passed |
329307 |
19.53 % |
| Transition |
C>T |
Passed |
286477 |
16.99 % |
| Transversion |
A>C |
Passed |
60976 |
3.62 % |
| Transversion |
C>A |
Passed |
54295 |
3.22 % |
| Transversion |
T>G |
Passed |
60932 |
3.61 % |
| Transversion |
G>T |
Passed |
54577 |
3.24 % |
| Transversion |
A>T |
Passed |
35524 |
2.11 % |
| Transversion |
T>A |
Passed |
35468 |
2.10 % |
| Transversion |
C>G |
Passed |
76052 |
4.51 % |
| Transversion |
G>C |
Passed |
76115 |
4.51 % |
| |
|
|
|
|
| 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 |
9.26 |
25302873 |
2733904 |
| Passed |
2.71 |
1232349 |
453939 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |