/EXTERNAL DEEP/variants/K006119_K006120_K006121_3_lane_gembs
BACK
SAMPLE K006119_K006120_K006121_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1169710120 |
843078094 |
72.08 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1169710120 |
100% |
1140703140 |
97.52 % |
29006980 |
2.48 % |
| |
|
|
|
|
|
|
| Passed |
847113383 |
72.42 % |
839202830 |
73.57 % |
7910553 |
0.93 % |
| Filtered |
322596737 |
27.58 % |
301500310 |
26.43 % |
21096427 |
2.49 % |
| |
|
|
|
|
|
|
| q20 |
281990515 |
87.41 % |
277181421 |
91.93 % |
4809094 |
22.80 % |
| q20,qd2 |
24782130 |
7.68 % |
9277255 |
3.08 % |
15504875 |
73.50 % |
| q20,mq40 |
8807296 |
2.73 % |
8686682 |
2.88 % |
120614 |
0.57 % |
| qd2 |
3218864 |
1.00 % |
2877257 |
0.95 % |
341607 |
1.62 % |
| q20,qd2,mq40 |
2796321 |
0.87 % |
2681862 |
0.89 % |
114459 |
0.54 % |
| mq40 |
968191 |
0.30 % |
770917 |
0.26 % |
197274 |
0.94 % |
| qd2,mq40 |
32035 |
0.01 % |
24916 |
0.01 % |
7119 |
0.03 % |
| qd2,fs60,mq40 |
596 |
0.00 % |
0 |
0.00 % |
596 |
0.00 % |
| qd2,fs60 |
278 |
0.00 % |
0 |
0.00 % |
278 |
0.00 % |
| fs60,mq40 |
229 |
0.00 % |
0 |
0.00 % |
229 |
0.00 % |
| fs60 |
190 |
0.00 % |
0 |
0.00 % |
190 |
0.00 % |
| q20,qd2,fs60 |
50 |
0.00 % |
0 |
0.00 % |
50 |
0.00 % |
| q20,qd2,fs60,mq40 |
40 |
0.00 % |
0 |
0.00 % |
40 |
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 |
9823655 |
31.87 % |
| Transition |
G>A |
All |
2396610 |
7.78 % |
| Transition |
T>C |
All |
11473273 |
37.23 % |
| Transition |
C>T |
All |
1657083 |
5.38 % |
| Transversion |
A>C |
All |
349344 |
1.13 % |
| Transversion |
C>A |
All |
1186304 |
3.85 % |
| Transversion |
T>G |
All |
439788 |
1.43 % |
| Transversion |
G>T |
All |
1100360 |
3.57 % |
| Transversion |
A>T |
All |
724417 |
2.35 % |
| Transversion |
T>A |
All |
829651 |
2.69 % |
| Transversion |
C>G |
All |
427322 |
1.39 % |
| Transversion |
G>C |
All |
412500 |
1.34 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
927350 |
19.17 % |
| Transition |
G>A |
Passed |
625442 |
12.93 % |
| Transition |
T>C |
Passed |
1429723 |
29.55 % |
| Transition |
C>T |
Passed |
553215 |
11.44 % |
| Transversion |
A>C |
Passed |
151376 |
3.13 % |
| Transversion |
C>A |
Passed |
192896 |
3.99 % |
| Transversion |
T>G |
Passed |
169077 |
3.50 % |
| Transversion |
G>T |
Passed |
170260 |
3.52 % |
| Transversion |
A>T |
Passed |
139404 |
2.88 % |
| Transversion |
T>A |
Passed |
163082 |
3.37 % |
| Transversion |
C>G |
Passed |
159093 |
3.29 % |
| Transversion |
G>C |
Passed |
156611 |
3.24 % |
| |
|
|
|
|
| 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 |
4.63 |
25350621 |
5469686 |
| Passed |
2.72 |
3535730 |
1301799 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |