/EXTERNAL DEEP/variants/K006093_K006094_K006095_3_lane_gembs
BACK
SAMPLE K006093_K006094_K006095_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1178847429 |
830151975 |
70.42 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1178847429 |
100% |
1141341293 |
96.82 % |
37506136 |
3.18 % |
| |
|
|
|
|
|
|
| Passed |
835520077 |
70.88 % |
825131746 |
72.29 % |
10388331 |
1.24 % |
| Filtered |
343327352 |
29.12 % |
316209547 |
27.71 % |
27117805 |
3.25 % |
| |
|
|
|
|
|
|
| q20 |
292438483 |
85.18 % |
285738608 |
90.36 % |
6699875 |
24.71 % |
| q20,qd2 |
30681054 |
8.94 % |
11312108 |
3.58 % |
19368946 |
71.43 % |
| q20,mq40 |
10367698 |
3.02 % |
10149951 |
3.21 % |
217747 |
0.80 % |
| qd2 |
5459667 |
1.59 % |
5065339 |
1.60 % |
394328 |
1.45 % |
| q20,qd2,mq40 |
3016144 |
0.88 % |
2848861 |
0.90 % |
167283 |
0.62 % |
| mq40 |
1300409 |
0.38 % |
1046508 |
0.33 % |
253901 |
0.94 % |
| qd2,mq40 |
57809 |
0.02 % |
48172 |
0.02 % |
9637 |
0.04 % |
| qd2,fs60 |
1992 |
0.00 % |
0 |
0.00 % |
1992 |
0.01 % |
| qd2,fs60,mq40 |
1639 |
0.00 % |
0 |
0.00 % |
1639 |
0.01 % |
| fs60 |
916 |
0.00 % |
0 |
0.00 % |
916 |
0.00 % |
| q20,qd2,fs60 |
754 |
0.00 % |
0 |
0.00 % |
754 |
0.00 % |
| fs60,mq40 |
486 |
0.00 % |
0 |
0.00 % |
486 |
0.00 % |
| q20,qd2,fs60,mq40 |
300 |
0.00 % |
0 |
0.00 % |
300 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
13307038 |
34.12 % |
| Transition |
G>A |
All |
2957999 |
7.59 % |
| Transition |
T>C |
All |
14624724 |
37.50 % |
| Transition |
C>T |
All |
2305338 |
5.91 % |
| Transversion |
A>C |
All |
532189 |
1.36 % |
| Transversion |
C>A |
All |
1129280 |
2.90 % |
| Transversion |
T>G |
All |
602417 |
1.54 % |
| Transversion |
G>T |
All |
1040124 |
2.67 % |
| Transversion |
A>T |
All |
721752 |
1.85 % |
| Transversion |
T>A |
All |
823934 |
2.11 % |
| Transversion |
C>G |
All |
485942 |
1.25 % |
| Transversion |
G>C |
All |
466337 |
1.20 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1112697 |
20.13 % |
| Transition |
G>A |
Passed |
686423 |
12.42 % |
| Transition |
T>C |
Passed |
1566668 |
28.34 % |
| Transition |
C>T |
Passed |
629058 |
11.38 % |
| Transversion |
A>C |
Passed |
187156 |
3.39 % |
| Transversion |
C>A |
Passed |
223855 |
4.05 % |
| Transversion |
T>G |
Passed |
200841 |
3.63 % |
| Transversion |
G>T |
Passed |
204248 |
3.69 % |
| Transversion |
A>T |
Passed |
159573 |
2.89 % |
| Transversion |
T>A |
Passed |
181366 |
3.28 % |
| Transversion |
C>G |
Passed |
189910 |
3.44 % |
| Transversion |
G>C |
Passed |
186388 |
3.37 % |
| |
|
|
|
|
| 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 |
5.72 |
33195099 |
5801975 |
| Passed |
2.61 |
3994846 |
1533337 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |