/EXTERNAL DEEP/variants/K006067_K006068_K006069_K006070_4_lane_gembs
BACK
SAMPLE K006067_K006068_K006069_K006070_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1167165098 |
962337377 |
82.45 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1167165098 |
100% |
1144281531 |
98.04 % |
22883567 |
1.96 % |
| |
|
|
|
|
|
|
| Passed |
964938112 |
82.67 % |
958595056 |
83.77 % |
6343056 |
0.66 % |
| Filtered |
202226986 |
17.33 % |
185686475 |
16.23 % |
16540511 |
1.71 % |
| |
|
|
|
|
|
|
| q20 |
165890491 |
82.03 % |
162887354 |
87.72 % |
3003137 |
18.16 % |
| q20,qd2 |
19727841 |
9.76 % |
7156633 |
3.85 % |
12571208 |
76.00 % |
| q20,mq40 |
8668855 |
4.29 % |
8543875 |
4.60 % |
124980 |
0.76 % |
| qd2 |
3918971 |
1.94 % |
3435896 |
1.85 % |
483075 |
2.92 % |
| q20,qd2,mq40 |
2659716 |
1.32 % |
2530005 |
1.36 % |
129711 |
0.78 % |
| mq40 |
1319476 |
0.65 % |
1101636 |
0.59 % |
217840 |
1.32 % |
| qd2,mq40 |
39469 |
0.02 % |
31076 |
0.02 % |
8393 |
0.05 % |
| qd2,fs60,mq40 |
828 |
0.00 % |
0 |
0.00 % |
828 |
0.01 % |
| qd2,fs60 |
465 |
0.00 % |
0 |
0.00 % |
465 |
0.00 % |
| fs60 |
340 |
0.00 % |
0 |
0.00 % |
340 |
0.00 % |
| fs60,mq40 |
334 |
0.00 % |
0 |
0.00 % |
334 |
0.00 % |
| q20,qd2,fs60 |
112 |
0.00 % |
0 |
0.00 % |
112 |
0.00 % |
| q20,qd2,fs60,mq40 |
85 |
0.00 % |
0 |
0.00 % |
85 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
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 |
8036621 |
32.54 % |
| Transition |
G>A |
All |
2099550 |
8.50 % |
| Transition |
T>C |
All |
9263103 |
37.50 % |
| Transition |
C>T |
All |
1461970 |
5.92 % |
| Transversion |
A>C |
All |
273141 |
1.11 % |
| Transversion |
C>A |
All |
768229 |
3.11 % |
| Transversion |
T>G |
All |
337328 |
1.37 % |
| Transversion |
G>T |
All |
709672 |
2.87 % |
| Transversion |
A>T |
All |
525661 |
2.13 % |
| Transversion |
T>A |
All |
590203 |
2.39 % |
| Transversion |
C>G |
All |
324495 |
1.31 % |
| Transversion |
G>C |
All |
309655 |
1.25 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
948051 |
19.47 % |
| Transition |
G>A |
Passed |
670314 |
13.76 % |
| Transition |
T>C |
Passed |
1343034 |
27.58 % |
| Transition |
C>T |
Passed |
605877 |
12.44 % |
| Transversion |
A>C |
Passed |
154577 |
3.17 % |
| Transversion |
C>A |
Passed |
187576 |
3.85 % |
| Transversion |
T>G |
Passed |
166332 |
3.42 % |
| Transversion |
G>T |
Passed |
169734 |
3.48 % |
| Transversion |
A>T |
Passed |
144854 |
2.97 % |
| Transversion |
T>A |
Passed |
161402 |
3.31 % |
| Transversion |
C>G |
Passed |
160697 |
3.30 % |
| Transversion |
G>C |
Passed |
158016 |
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 |
5.43 |
20861244 |
3838384 |
| Passed |
2.74 |
3567276 |
1303188 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |