/EXTERNAL BLUEPRINT/variants/K010530_1_lane_gembs
BACK
SAMPLE K010530_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1106165185 |
182763099 |
16.52 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1106165185 |
100% |
1080763917 |
97.70 % |
25401268 |
2.30 % |
| |
|
|
|
|
|
|
| Passed |
191296746 |
17.29 % |
181797181 |
16.82 % |
9499565 |
4.97 % |
| Filtered |
914868439 |
82.71 % |
898966736 |
83.18 % |
15901703 |
8.31 % |
| |
|
|
|
|
|
|
| q20 |
829181318 |
90.63 % |
822669187 |
91.51 % |
6512131 |
40.95 % |
| q20,qd2 |
67328395 |
7.36 % |
58183957 |
6.47 % |
9144438 |
57.51 % |
| q20,mq40 |
12361854 |
1.35 % |
12279224 |
1.37 % |
82630 |
0.52 % |
| q20,qd2,mq40 |
5666265 |
0.62 % |
5612522 |
0.62 % |
53743 |
0.34 % |
| mq40 |
264731 |
0.03 % |
164266 |
0.02 % |
100465 |
0.63 % |
| qd2 |
52956 |
0.01 % |
47134 |
0.01 % |
5822 |
0.04 % |
| qd2,mq40 |
12629 |
0.00 % |
10446 |
0.00 % |
2183 |
0.01 % |
| qd2,fs60,mq40 |
149 |
0.00 % |
0 |
0.00 % |
149 |
0.00 % |
| fs60,mq40 |
57 |
0.00 % |
0 |
0.00 % |
57 |
0.00 % |
| qd2,fs60 |
44 |
0.00 % |
0 |
0.00 % |
44 |
0.00 % |
| q20,qd2,fs60,mq40 |
29 |
0.00 % |
0 |
0.00 % |
29 |
0.00 % |
| fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
8309410 |
30.20 % |
| Transition |
G>A |
All |
1206178 |
4.38 % |
| Transition |
T>C |
All |
8353117 |
30.36 % |
| Transition |
C>T |
All |
1207678 |
4.39 % |
| Transversion |
A>C |
All |
435817 |
1.58 % |
| Transversion |
C>A |
All |
1489402 |
5.41 % |
| Transversion |
T>G |
All |
433592 |
1.58 % |
| Transversion |
G>T |
All |
1478676 |
5.37 % |
| Transversion |
A>T |
All |
1973047 |
7.17 % |
| Transversion |
T>A |
All |
1986270 |
7.22 % |
| Transversion |
C>G |
All |
317562 |
1.15 % |
| Transversion |
G>C |
All |
319947 |
1.16 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
217008 |
18.76 % |
| Transition |
G>A |
Passed |
165844 |
14.34 % |
| Transition |
T>C |
Passed |
215888 |
18.66 % |
| Transition |
C>T |
Passed |
166303 |
14.38 % |
| Transversion |
A>C |
Passed |
48610 |
4.20 % |
| Transversion |
C>A |
Passed |
52627 |
4.55 % |
| Transversion |
T>G |
Passed |
48810 |
4.22 % |
| Transversion |
G>T |
Passed |
51818 |
4.48 % |
| Transversion |
A>T |
Passed |
49452 |
4.27 % |
| Transversion |
T>A |
Passed |
49849 |
4.31 % |
| Transversion |
C>G |
Passed |
45388 |
3.92 % |
| Transversion |
G>C |
Passed |
45275 |
3.91 % |
| |
|
|
|
|
| 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 |
2.26 |
19076383 |
8434313 |
| Passed |
1.95 |
765043 |
391829 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |