/EXTERNAL DEEP/variants/K006075_K006076_K006077_3_lane_gembs
BACK
SAMPLE K006075_K006076_K006077_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170667545 |
855941491 |
73.12 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170667545 |
100% |
1141898890 |
97.54 % |
28768655 |
2.46 % |
| |
|
|
|
|
|
|
| Passed |
859882174 |
73.45 % |
851929331 |
74.61 % |
7952843 |
0.92 % |
| Filtered |
310785371 |
26.55 % |
289969559 |
25.39 % |
20815812 |
2.42 % |
| |
|
|
|
|
|
|
| q20 |
269630696 |
86.76 % |
264576122 |
91.24 % |
5054574 |
24.28 % |
| q20,qd2 |
24182181 |
7.78 % |
9256763 |
3.19 % |
14925418 |
71.70 % |
| q20,mq40 |
8984641 |
2.89 % |
8853917 |
3.05 % |
130724 |
0.63 % |
| qd2 |
4047970 |
1.30 % |
3683120 |
1.27 % |
364850 |
1.75 % |
| q20,qd2,mq40 |
2794288 |
0.90 % |
2670812 |
0.92 % |
123476 |
0.59 % |
| mq40 |
1109429 |
0.36 % |
901689 |
0.31 % |
207740 |
1.00 % |
| qd2,mq40 |
34577 |
0.01 % |
27136 |
0.01 % |
7441 |
0.04 % |
| qd2,fs60,mq40 |
663 |
0.00 % |
0 |
0.00 % |
663 |
0.00 % |
| qd2,fs60 |
287 |
0.00 % |
0 |
0.00 % |
287 |
0.00 % |
| fs60 |
242 |
0.00 % |
0 |
0.00 % |
242 |
0.00 % |
| fs60,mq40 |
241 |
0.00 % |
0 |
0.00 % |
241 |
0.00 % |
| q20,qd2,fs60 |
86 |
0.00 % |
0 |
0.00 % |
86 |
0.00 % |
| q20,qd2,fs60,mq40 |
68 |
0.00 % |
0 |
0.00 % |
68 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
9905240 |
32.38 % |
| Transition |
G>A |
All |
2388232 |
7.81 % |
| Transition |
T>C |
All |
11608203 |
37.95 % |
| Transition |
C>T |
All |
1708632 |
5.59 % |
| Transversion |
A>C |
All |
359026 |
1.17 % |
| Transversion |
C>A |
All |
1003303 |
3.28 % |
| Transversion |
T>G |
All |
435950 |
1.43 % |
| Transversion |
G>T |
All |
940475 |
3.07 % |
| Transversion |
A>T |
All |
670864 |
2.19 % |
| Transversion |
T>A |
All |
753401 |
2.46 % |
| Transversion |
C>G |
All |
415628 |
1.36 % |
| Transversion |
G>C |
All |
401341 |
1.31 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
972681 |
19.51 % |
| Transition |
G>A |
Passed |
624926 |
12.53 % |
| Transition |
T>C |
Passed |
1554472 |
31.18 % |
| Transition |
C>T |
Passed |
555187 |
11.14 % |
| Transversion |
A>C |
Passed |
152157 |
3.05 % |
| Transversion |
C>A |
Passed |
184269 |
3.70 % |
| Transversion |
T>G |
Passed |
166782 |
3.35 % |
| Transversion |
G>T |
Passed |
165682 |
3.32 % |
| Transversion |
A>T |
Passed |
137848 |
2.76 % |
| Transversion |
T>A |
Passed |
157286 |
3.15 % |
| Transversion |
C>G |
Passed |
158238 |
3.17 % |
| Transversion |
G>C |
Passed |
156389 |
3.14 % |
| |
|
|
|
|
| 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 |
5.14 |
25610307 |
4979988 |
| Passed |
2.90 |
3707266 |
1278651 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |