/EXTERNAL BLUEPRINT/variants/K006382_K006412_20_lane_gembs
BACK
SAMPLE K006382_K006412_20_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158880981 |
1024296729 |
88.39 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158880981 |
100% |
1146291306 |
98.91 % |
12589675 |
1.09 % |
| |
|
|
|
|
|
|
| Passed |
1025577425 |
88.50 % |
1021351951 |
89.10 % |
4225474 |
0.41 % |
| Filtered |
133303556 |
11.50 % |
124939355 |
10.90 % |
8364201 |
0.82 % |
| |
|
|
|
|
|
|
| q20 |
95572605 |
71.70 % |
94599646 |
75.72 % |
972959 |
11.63 % |
| q20,mq40 |
11556031 |
8.67 % |
11457605 |
9.17 % |
98426 |
1.18 % |
| q20,qd2 |
10004935 |
7.51 % |
3301073 |
2.64 % |
6703862 |
80.15 % |
| mq40 |
7660904 |
5.75 % |
7443781 |
5.96 % |
217123 |
2.60 % |
| qd2 |
5658873 |
4.25 % |
5493962 |
4.40 % |
164911 |
1.97 % |
| q20,qd2,mq40 |
2723818 |
2.04 % |
2545744 |
2.04 % |
178074 |
2.13 % |
| qd2,mq40 |
114086 |
0.09 % |
97544 |
0.08 % |
16542 |
0.20 % |
| fs60 |
3398 |
0.00 % |
0 |
0.00 % |
3398 |
0.04 % |
| qd2,fs60 |
3284 |
0.00 % |
0 |
0.00 % |
3284 |
0.04 % |
| qd2,fs60,mq40 |
2336 |
0.00 % |
0 |
0.00 % |
2336 |
0.03 % |
| q20,qd2,fs60 |
2243 |
0.00 % |
0 |
0.00 % |
2243 |
0.03 % |
| fs60,mq40 |
721 |
0.00 % |
0 |
0.00 % |
721 |
0.01 % |
| q20,qd2,fs60,mq40 |
313 |
0.00 % |
0 |
0.00 % |
313 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
4661670 |
32.72 % |
| Transition |
G>A |
All |
1206630 |
8.47 % |
| Transition |
T>C |
All |
4610937 |
32.37 % |
| Transition |
C>T |
All |
1221107 |
8.57 % |
| Transversion |
A>C |
All |
231306 |
1.62 % |
| Transversion |
C>A |
All |
449853 |
3.16 % |
| Transversion |
T>G |
All |
234057 |
1.64 % |
| Transversion |
G>T |
All |
445973 |
3.13 % |
| Transversion |
A>T |
All |
375410 |
2.64 % |
| Transversion |
T>A |
All |
366235 |
2.57 % |
| Transversion |
C>G |
All |
222069 |
1.56 % |
| Transversion |
G>C |
All |
219834 |
1.54 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
677677 |
17.04 % |
| Transition |
G>A |
Passed |
662429 |
16.66 % |
| Transition |
T>C |
Passed |
679427 |
17.08 % |
| Transition |
C>T |
Passed |
667289 |
16.78 % |
| Transversion |
A>C |
Passed |
165998 |
4.17 % |
| Transversion |
C>A |
Passed |
168051 |
4.23 % |
| Transversion |
T>G |
Passed |
165925 |
4.17 % |
| Transversion |
G>T |
Passed |
168402 |
4.23 % |
| Transversion |
A>T |
Passed |
143547 |
3.61 % |
| Transversion |
T>A |
Passed |
143595 |
3.61 % |
| Transversion |
C>G |
Passed |
167335 |
4.21 % |
| Transversion |
G>C |
Passed |
167507 |
4.21 % |
| |
|
|
|
|
| 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 |
4.60 |
11700344 |
2544737 |
| Passed |
2.08 |
2686822 |
1290360 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |