/EXTERNAL BLUEPRINT/variants/K006383_K006413_19_lane_gembs
BACK
SAMPLE K006383_K006413_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158403152 |
1027300454 |
88.68 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158403152 |
100% |
1146527196 |
98.97 % |
11875956 |
1.03 % |
| |
|
|
|
|
|
|
| Passed |
1028539088 |
88.79 % |
1024916609 |
89.39 % |
3622479 |
0.35 % |
| Filtered |
129864064 |
11.21 % |
121610587 |
10.61 % |
8253477 |
0.80 % |
| |
|
|
|
|
|
|
| q20 |
93913279 |
72.32 % |
92993825 |
76.47 % |
919454 |
11.14 % |
| q20,mq40 |
11360999 |
8.75 % |
11269110 |
9.27 % |
91889 |
1.11 % |
| q20,qd2 |
9804137 |
7.55 % |
3112983 |
2.56 % |
6691154 |
81.07 % |
| mq40 |
7559177 |
5.82 % |
7359749 |
6.05 % |
199428 |
2.42 % |
| qd2 |
4431572 |
3.41 % |
4281993 |
3.52 % |
149579 |
1.81 % |
| q20,qd2,mq40 |
2670629 |
2.06 % |
2496705 |
2.05 % |
173924 |
2.11 % |
| qd2,mq40 |
112162 |
0.09 % |
96222 |
0.08 % |
15940 |
0.19 % |
| fs60 |
3435 |
0.00 % |
0 |
0.00 % |
3435 |
0.04 % |
| qd2,fs60 |
2878 |
0.00 % |
0 |
0.00 % |
2878 |
0.03 % |
| q20,qd2,fs60 |
2381 |
0.00 % |
0 |
0.00 % |
2381 |
0.03 % |
| qd2,fs60,mq40 |
2313 |
0.00 % |
0 |
0.00 % |
2313 |
0.03 % |
| fs60,mq40 |
777 |
0.00 % |
0 |
0.00 % |
777 |
0.01 % |
| q20,qd2,fs60,mq40 |
318 |
0.00 % |
0 |
0.00 % |
318 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60 |
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 |
4604488 |
33.76 % |
| Transition |
G>A |
All |
1048888 |
7.69 % |
| Transition |
T>C |
All |
4563025 |
33.46 % |
| Transition |
C>T |
All |
1047395 |
7.68 % |
| Transversion |
A>C |
All |
211374 |
1.55 % |
| Transversion |
C>A |
All |
424346 |
3.11 % |
| Transversion |
T>G |
All |
214432 |
1.57 % |
| Transversion |
G>T |
All |
417490 |
3.06 % |
| Transversion |
A>T |
All |
356926 |
2.62 % |
| Transversion |
T>A |
All |
351992 |
2.58 % |
| Transversion |
C>G |
All |
199915 |
1.47 % |
| Transversion |
G>C |
All |
197492 |
1.45 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
607751 |
17.26 % |
| Transition |
G>A |
Passed |
577597 |
16.41 % |
| Transition |
T>C |
Passed |
609535 |
17.31 % |
| Transition |
C>T |
Passed |
578983 |
16.45 % |
| Transversion |
A>C |
Passed |
148856 |
4.23 % |
| Transversion |
C>A |
Passed |
149021 |
4.23 % |
| Transversion |
T>G |
Passed |
149500 |
4.25 % |
| Transversion |
G>T |
Passed |
148575 |
4.22 % |
| Transversion |
A>T |
Passed |
127286 |
3.62 % |
| Transversion |
T>A |
Passed |
127799 |
3.63 % |
| Transversion |
C>G |
Passed |
147612 |
4.19 % |
| Transversion |
G>C |
Passed |
148020 |
4.20 % |
| |
|
|
|
|
| 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 |
4.74 |
11263796 |
2373967 |
| Passed |
2.07 |
2373866 |
1146669 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |