/EXTERNAL BLUEPRINT/variants/K006392_K006405_20_lane_gembs
BACK
SAMPLE K006392_K006405_20_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1152479237 |
1042418825 |
90.45 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1152479237 |
100% |
1141597225 |
99.06 % |
10882012 |
0.94 % |
| |
|
|
|
|
|
|
| Passed |
1043378498 |
90.53 % |
1040001292 |
91.10 % |
3377206 |
0.32 % |
| Filtered |
109100739 |
9.47 % |
101595933 |
8.90 % |
7504806 |
0.72 % |
| |
|
|
|
|
|
|
| q20 |
72287042 |
66.26 % |
71487536 |
70.36 % |
799506 |
10.65 % |
| q20,mq40 |
11390353 |
10.44 % |
11286765 |
11.11 % |
103588 |
1.38 % |
| q20,qd2 |
9004848 |
8.25 % |
2996867 |
2.95 % |
6007981 |
80.06 % |
| mq40 |
7277445 |
6.67 % |
7063604 |
6.95 % |
213841 |
2.85 % |
| qd2 |
6222846 |
5.70 % |
6064168 |
5.97 % |
158678 |
2.11 % |
| q20,qd2,mq40 |
2785987 |
2.55 % |
2595522 |
2.55 % |
190465 |
2.54 % |
| qd2,mq40 |
119002 |
0.11 % |
101471 |
0.10 % |
17531 |
0.23 % |
| fs60 |
3816 |
0.00 % |
0 |
0.00 % |
3816 |
0.05 % |
| q20,qd2,fs60 |
2870 |
0.00 % |
0 |
0.00 % |
2870 |
0.04 % |
| qd2,fs60 |
2844 |
0.00 % |
0 |
0.00 % |
2844 |
0.04 % |
| qd2,fs60,mq40 |
2396 |
0.00 % |
0 |
0.00 % |
2396 |
0.03 % |
| fs60,mq40 |
932 |
0.00 % |
0 |
0.00 % |
932 |
0.01 % |
| q20,qd2,fs60,mq40 |
348 |
0.00 % |
0 |
0.00 % |
348 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
4074730 |
32.24 % |
| Transition |
G>A |
All |
1062705 |
8.41 % |
| Transition |
T>C |
All |
4041478 |
31.97 % |
| Transition |
C>T |
All |
1070540 |
8.47 % |
| Transversion |
A>C |
All |
214747 |
1.70 % |
| Transversion |
C>A |
All |
432304 |
3.42 % |
| Transversion |
T>G |
All |
218635 |
1.73 % |
| Transversion |
G>T |
All |
425305 |
3.36 % |
| Transversion |
A>T |
All |
350032 |
2.77 % |
| Transversion |
T>A |
All |
345276 |
2.73 % |
| Transversion |
C>G |
All |
203308 |
1.61 % |
| Transversion |
G>C |
All |
200553 |
1.59 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
614595 |
17.24 % |
| Transition |
G>A |
Passed |
585343 |
16.42 % |
| Transition |
T>C |
Passed |
616542 |
17.30 % |
| Transition |
C>T |
Passed |
588230 |
16.50 % |
| Transversion |
A>C |
Passed |
150706 |
4.23 % |
| Transversion |
C>A |
Passed |
150487 |
4.22 % |
| Transversion |
T>G |
Passed |
151299 |
4.24 % |
| Transversion |
G>T |
Passed |
150638 |
4.23 % |
| Transversion |
A>T |
Passed |
129256 |
3.63 % |
| Transversion |
T>A |
Passed |
129185 |
3.62 % |
| Transversion |
C>G |
Passed |
148971 |
4.18 % |
| Transversion |
G>C |
Passed |
149363 |
4.19 % |
| |
|
|
|
|
| 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 |
4.29 |
10249453 |
2390160 |
| Passed |
2.07 |
2404710 |
1159905 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |