/EXTERNAL DEEP/variants/K006115_K006116_K006117_K006118_4_lane_gembs
BACK
SAMPLE K006115_K006116_K006117_K006118_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1164717337 |
1001730214 |
86.01 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1164717337 |
100% |
1145515241 |
98.35 % |
19202096 |
1.65 % |
| |
|
|
|
|
|
|
| Passed |
1003507113 |
86.16 % |
998091877 |
87.13 % |
5415236 |
0.54 % |
| Filtered |
161210224 |
13.84 % |
147423364 |
12.87 % |
13786860 |
1.37 % |
| |
|
|
|
|
|
|
| q20 |
126720673 |
78.61 % |
124501817 |
84.45 % |
2218856 |
16.09 % |
| q20,qd2 |
17333576 |
10.75 % |
6768793 |
4.59 % |
10564783 |
76.63 % |
| q20,mq40 |
8616566 |
5.34 % |
8482160 |
5.75 % |
134406 |
0.97 % |
| qd2 |
4439205 |
2.75 % |
3941209 |
2.67 % |
497996 |
3.61 % |
| q20,qd2,mq40 |
2591664 |
1.61 % |
2452608 |
1.66 % |
139056 |
1.01 % |
| mq40 |
1463937 |
0.91 % |
1243483 |
0.84 % |
220454 |
1.60 % |
| qd2,mq40 |
42353 |
0.03 % |
33294 |
0.02 % |
9059 |
0.07 % |
| qd2,fs60,mq40 |
870 |
0.00 % |
0 |
0.00 % |
870 |
0.01 % |
| qd2,fs60 |
516 |
0.00 % |
0 |
0.00 % |
516 |
0.00 % |
| fs60 |
361 |
0.00 % |
0 |
0.00 % |
361 |
0.00 % |
| fs60,mq40 |
331 |
0.00 % |
0 |
0.00 % |
331 |
0.00 % |
| q20,qd2,fs60 |
95 |
0.00 % |
0 |
0.00 % |
95 |
0.00 % |
| q20,qd2,fs60,mq40 |
75 |
0.00 % |
0 |
0.00 % |
75 |
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 |
6498968 |
30.94 % |
| Transition |
G>A |
All |
1923554 |
9.16 % |
| Transition |
T>C |
All |
7575512 |
36.07 % |
| Transition |
C>T |
All |
1351399 |
6.43 % |
| Transversion |
A>C |
All |
268862 |
1.28 % |
| Transversion |
C>A |
All |
711374 |
3.39 % |
| Transversion |
T>G |
All |
322140 |
1.53 % |
| Transversion |
G>T |
All |
661452 |
3.15 % |
| Transversion |
A>T |
All |
516416 |
2.46 % |
| Transversion |
T>A |
All |
569502 |
2.71 % |
| Transversion |
C>G |
All |
308063 |
1.47 % |
| Transversion |
G>C |
All |
296633 |
1.41 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
920513 |
19.12 % |
| Transition |
G>A |
Passed |
686985 |
14.27 % |
| Transition |
T>C |
Passed |
1262945 |
26.23 % |
| Transition |
C>T |
Passed |
618561 |
12.85 % |
| Transversion |
A>C |
Passed |
158772 |
3.30 % |
| Transversion |
C>A |
Passed |
189273 |
3.93 % |
| Transversion |
T>G |
Passed |
168220 |
3.49 % |
| Transversion |
G>T |
Passed |
172193 |
3.58 % |
| Transversion |
A>T |
Passed |
147825 |
3.07 % |
| Transversion |
T>A |
Passed |
163396 |
3.39 % |
| Transversion |
C>G |
Passed |
163804 |
3.40 % |
| Transversion |
G>C |
Passed |
161893 |
3.36 % |
| |
|
|
|
|
| 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 |
4.75 |
17349433 |
3654442 |
| Passed |
2.63 |
3489004 |
1325376 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |