/EXTERNAL DEEP/variants/K006078_K006079_K006080_3_lane_gembs
BACK
SAMPLE K006078_K006079_K006080_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1168139274 |
869958867 |
74.47 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1168139274 |
100% |
1142122291 |
97.77 % |
26016983 |
2.23 % |
| |
|
|
|
|
|
|
| Passed |
873509930 |
74.78 % |
866153321 |
75.84 % |
7356609 |
0.84 % |
| Filtered |
294629344 |
25.22 % |
275968970 |
24.16 % |
18660374 |
2.14 % |
| |
|
|
|
|
|
|
| q20 |
257554448 |
87.42 % |
253413468 |
91.83 % |
4140980 |
22.19 % |
| q20,qd2 |
21650622 |
7.35 % |
7898278 |
2.86 % |
13752344 |
73.70 % |
| q20,mq40 |
8610518 |
2.92 % |
8497665 |
3.08 % |
112853 |
0.60 % |
| qd2 |
3034742 |
1.03 % |
2684173 |
0.97 % |
350569 |
1.88 % |
| q20,qd2,mq40 |
2719760 |
0.92 % |
2612307 |
0.95 % |
107453 |
0.58 % |
| mq40 |
1024546 |
0.35 % |
837183 |
0.30 % |
187363 |
1.00 % |
| qd2,mq40 |
33247 |
0.01 % |
25896 |
0.01 % |
7351 |
0.04 % |
| qd2,fs60,mq40 |
608 |
0.00 % |
0 |
0.00 % |
608 |
0.00 % |
| qd2,fs60 |
272 |
0.00 % |
0 |
0.00 % |
272 |
0.00 % |
| fs60,mq40 |
223 |
0.00 % |
0 |
0.00 % |
223 |
0.00 % |
| fs60 |
215 |
0.00 % |
0 |
0.00 % |
215 |
0.00 % |
| q20,qd2,fs60 |
71 |
0.00 % |
0 |
0.00 % |
71 |
0.00 % |
| q20,qd2,fs60,mq40 |
69 |
0.00 % |
0 |
0.00 % |
69 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
9337306 |
33.57 % |
| Transition |
G>A |
All |
2002551 |
7.20 % |
| Transition |
T>C |
All |
10712928 |
38.51 % |
| Transition |
C>T |
All |
1559474 |
5.61 % |
| Transversion |
A>C |
All |
312234 |
1.12 % |
| Transversion |
C>A |
All |
824764 |
2.96 % |
| Transversion |
T>G |
All |
362412 |
1.30 % |
| Transversion |
G>T |
All |
788481 |
2.83 % |
| Transversion |
A>T |
All |
591034 |
2.12 % |
| Transversion |
T>A |
All |
640877 |
2.30 % |
| Transversion |
C>G |
All |
345836 |
1.24 % |
| Transversion |
G>C |
All |
339791 |
1.22 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
945279 |
19.70 % |
| Transition |
G>A |
Passed |
612643 |
12.76 % |
| Transition |
T>C |
Passed |
1425759 |
29.71 % |
| Transition |
C>T |
Passed |
560047 |
11.67 % |
| Transversion |
A>C |
Passed |
151150 |
3.15 % |
| Transversion |
C>A |
Passed |
180366 |
3.76 % |
| Transversion |
T>G |
Passed |
161301 |
3.36 % |
| Transversion |
G>T |
Passed |
166024 |
3.46 % |
| Transversion |
A>T |
Passed |
137191 |
2.86 % |
| Transversion |
T>A |
Passed |
150085 |
3.13 % |
| Transversion |
C>G |
Passed |
155404 |
3.24 % |
| Transversion |
G>C |
Passed |
154203 |
3.21 % |
| |
|
|
|
|
| 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 |
5.61 |
23612259 |
4205429 |
| Passed |
2.82 |
3543728 |
1255724 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |