/EXTERNAL BLUEPRINT/variants/K006265_7_lane_gembs
BACK
SAMPLE K006265_7_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1116708181 |
659040005 |
59.02 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1116708181 |
100% |
1096826702 |
98.22 % |
19881479 |
1.78 % |
| |
|
|
|
|
|
|
| Passed |
660386049 |
59.14 % |
657761014 |
59.97 % |
2625035 |
0.40 % |
| Filtered |
456322132 |
40.86 % |
439065688 |
40.03 % |
17256444 |
2.61 % |
| |
|
|
|
|
|
|
| q20 |
340922702 |
74.71 % |
338740853 |
77.15 % |
2181849 |
12.64 % |
| q20,qd2 |
50553773 |
11.08 % |
36250519 |
8.26 % |
14303254 |
82.89 % |
| qd2 |
37624533 |
8.25 % |
37459984 |
8.53 % |
164549 |
0.95 % |
| q20,mq40 |
13565554 |
2.97 % |
13440857 |
3.06 % |
124697 |
0.72 % |
| mq40 |
10323972 |
2.26 % |
10118629 |
2.30 % |
205343 |
1.19 % |
| q20,qd2,mq40 |
3145203 |
0.69 % |
2905651 |
0.66 % |
239552 |
1.39 % |
| qd2,mq40 |
165425 |
0.04 % |
149195 |
0.03 % |
16230 |
0.09 % |
| q20,qd2,fs60 |
7197 |
0.00 % |
0 |
0.00 % |
7197 |
0.04 % |
| qd2,fs60 |
5309 |
0.00 % |
0 |
0.00 % |
5309 |
0.03 % |
| fs60 |
4191 |
0.00 % |
0 |
0.00 % |
4191 |
0.02 % |
| qd2,fs60,mq40 |
2471 |
0.00 % |
0 |
0.00 % |
2471 |
0.01 % |
| q20,qd2,fs60,mq40 |
938 |
0.00 % |
0 |
0.00 % |
938 |
0.01 % |
| fs60,mq40 |
848 |
0.00 % |
0 |
0.00 % |
848 |
0.00 % |
| q20,fs60 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
2795638 |
6.75 % |
| Transition |
G>A |
All |
16783287 |
40.55 % |
| Transition |
T>C |
All |
2590466 |
6.26 % |
| Transition |
C>T |
All |
16687493 |
40.32 % |
| Transversion |
A>C |
All |
199827 |
0.48 % |
| Transversion |
C>A |
All |
488208 |
1.18 % |
| Transversion |
T>G |
All |
214047 |
0.52 % |
| Transversion |
G>T |
All |
481409 |
1.16 % |
| Transversion |
A>T |
All |
386581 |
0.93 % |
| Transversion |
T>A |
All |
380932 |
0.92 % |
| Transversion |
C>G |
All |
194232 |
0.47 % |
| Transversion |
G>C |
All |
185074 |
0.45 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
377154 |
18.96 % |
| Transition |
G>A |
Passed |
341583 |
17.17 % |
| Transition |
T>C |
Passed |
375282 |
18.86 % |
| Transition |
C>T |
Passed |
341249 |
17.15 % |
| Transversion |
A>C |
Passed |
73232 |
3.68 % |
| Transversion |
C>A |
Passed |
67434 |
3.39 % |
| Transversion |
T>G |
Passed |
73389 |
3.69 % |
| Transversion |
G>T |
Passed |
67509 |
3.39 % |
| Transversion |
A>T |
Passed |
47825 |
2.40 % |
| Transversion |
T>A |
Passed |
47796 |
2.40 % |
| Transversion |
C>G |
Passed |
88402 |
4.44 % |
| Transversion |
G>C |
Passed |
88832 |
4.46 % |
| |
|
|
|
|
| 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 |
15.36 |
38856884 |
2530310 |
| Passed |
2.59 |
1435268 |
554419 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |