/EXTERNAL BLUEPRINT/variants/K006261_19_lane_gembs
BACK
SAMPLE K006261_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1154778048 |
936937827 |
81.14 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1154778048 |
100% |
1143217835 |
99.00 % |
11560213 |
1.00 % |
| |
|
|
|
|
|
|
| Passed |
938330989 |
81.26 % |
934896250 |
81.78 % |
3434739 |
0.37 % |
| Filtered |
216447059 |
18.74 % |
208321585 |
18.22 % |
8125474 |
0.87 % |
| |
|
|
|
|
|
|
| q20 |
172784589 |
79.83 % |
171758497 |
82.45 % |
1026092 |
12.63 % |
| q20,mq40 |
14394744 |
6.65 % |
14273662 |
6.85 % |
121082 |
1.49 % |
| q20,qd2 |
14012774 |
6.47 % |
7685406 |
3.69 % |
6327368 |
77.87 % |
| mq40 |
9389473 |
4.34 % |
9143121 |
4.39 % |
246352 |
3.03 % |
| q20,qd2,mq40 |
2963718 |
1.37 % |
2723814 |
1.31 % |
239904 |
2.95 % |
| qd2 |
2774379 |
1.28 % |
2633633 |
1.26 % |
140746 |
1.73 % |
| qd2,mq40 |
118863 |
0.05 % |
103452 |
0.05 % |
15411 |
0.19 % |
| q20,qd2,fs60 |
2932 |
0.00 % |
0 |
0.00 % |
2932 |
0.04 % |
| qd2,fs60,mq40 |
1776 |
0.00 % |
0 |
0.00 % |
1776 |
0.02 % |
| fs60 |
1496 |
0.00 % |
0 |
0.00 % |
1496 |
0.02 % |
| qd2,fs60 |
1156 |
0.00 % |
0 |
0.00 % |
1156 |
0.01 % |
| fs60,mq40 |
693 |
0.00 % |
0 |
0.00 % |
693 |
0.01 % |
| q20,qd2,fs60,mq40 |
460 |
0.00 % |
0 |
0.00 % |
460 |
0.01 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
3216104 |
23.64 % |
| Transition |
G>A |
All |
2426098 |
17.83 % |
| Transition |
T>C |
All |
3152006 |
23.17 % |
| Transition |
C>T |
All |
2349816 |
17.27 % |
| Transversion |
A>C |
All |
204266 |
1.50 % |
| Transversion |
C>A |
All |
469379 |
3.45 % |
| Transversion |
T>G |
All |
209893 |
1.54 % |
| Transversion |
G>T |
All |
471077 |
3.46 % |
| Transversion |
A>T |
All |
361762 |
2.66 % |
| Transversion |
T>A |
All |
349605 |
2.57 % |
| Transversion |
C>G |
All |
199909 |
1.47 % |
| Transversion |
G>C |
All |
196491 |
1.44 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
539997 |
17.61 % |
| Transition |
G>A |
Passed |
514505 |
16.78 % |
| Transition |
T>C |
Passed |
544143 |
17.74 % |
| Transition |
C>T |
Passed |
516433 |
16.84 % |
| Transversion |
A>C |
Passed |
122437 |
3.99 % |
| Transversion |
C>A |
Passed |
123089 |
4.01 % |
| Transversion |
T>G |
Passed |
122319 |
3.99 % |
| Transversion |
G>T |
Passed |
122753 |
4.00 % |
| Transversion |
A>T |
Passed |
98313 |
3.21 % |
| Transversion |
T>A |
Passed |
97929 |
3.19 % |
| Transversion |
C>G |
Passed |
132273 |
4.31 % |
| Transversion |
G>C |
Passed |
132597 |
4.32 % |
| |
|
|
|
|
| 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 |
4.53 |
11144024 |
2462382 |
| Passed |
2.22 |
2115078 |
951710 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |