/EXTERNAL DEEP/variants/K008974_K008975_K008976_K008977_K008978_K008979_K008980_K008981_7_lane_gembs
BACK
SAMPLE K008974_K008975_K008976_K008977_K008978_K008979_K008980_K008981_7_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1172193403 |
547220856 |
46.68 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1172193403 |
100% |
1125133412 |
95.99 % |
47059991 |
4.01 % |
| |
|
|
|
|
|
|
| Passed |
557979825 |
47.60 % |
541783915 |
48.15 % |
16195910 |
2.90 % |
| Filtered |
614213578 |
52.40 % |
583349497 |
51.85 % |
30864081 |
5.53 % |
| |
|
|
|
|
|
|
| q20 |
554448104 |
90.27 % |
544496056 |
93.34 % |
9952048 |
32.24 % |
| q20,qd2 |
33897600 |
5.52 % |
14407618 |
2.47 % |
19489982 |
63.15 % |
| q20,mq40 |
17999026 |
2.93 % |
17643936 |
3.02 % |
355090 |
1.15 % |
| q20,qd2,mq40 |
4324038 |
0.70 % |
4015430 |
0.69 % |
308608 |
1.00 % |
| mq40 |
2007412 |
0.33 % |
1430832 |
0.25 % |
576580 |
1.87 % |
| qd2 |
1504408 |
0.24 % |
1331155 |
0.23 % |
173253 |
0.56 % |
| qd2,mq40 |
32655 |
0.01 % |
24470 |
0.00 % |
8185 |
0.03 % |
| fs60,mq40 |
117 |
0.00 % |
0 |
0.00 % |
117 |
0.00 % |
| qd2,fs60,mq40 |
103 |
0.00 % |
0 |
0.00 % |
103 |
0.00 % |
| qd2,fs60 |
65 |
0.00 % |
0 |
0.00 % |
65 |
0.00 % |
| fs60 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| q20,qd2,fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
14990446 |
30.91 % |
| Transition |
G>A |
All |
3194791 |
6.59 % |
| Transition |
T>C |
All |
15893320 |
32.78 % |
| Transition |
C>T |
All |
2591896 |
5.35 % |
| Transversion |
A>C |
All |
911154 |
1.88 % |
| Transversion |
C>A |
All |
2461869 |
5.08 % |
| Transversion |
T>G |
All |
1045232 |
2.16 % |
| Transversion |
G>T |
All |
2269026 |
4.68 % |
| Transversion |
A>T |
All |
1612390 |
3.33 % |
| Transversion |
T>A |
All |
1838690 |
3.79 % |
| Transversion |
C>G |
All |
849843 |
1.75 % |
| Transversion |
G>C |
All |
830833 |
1.71 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1210452 |
21.53 % |
| Transition |
G>A |
Passed |
631131 |
11.23 % |
| Transition |
T>C |
Passed |
1515647 |
26.96 % |
| Transition |
C>T |
Passed |
527867 |
9.39 % |
| Transversion |
A>C |
Passed |
195898 |
3.48 % |
| Transversion |
C>A |
Passed |
278788 |
4.96 % |
| Transversion |
T>G |
Passed |
218319 |
3.88 % |
| Transversion |
G>T |
Passed |
240181 |
4.27 % |
| Transversion |
A>T |
Passed |
158090 |
2.81 % |
| Transversion |
T>A |
Passed |
202129 |
3.60 % |
| Transversion |
C>G |
Passed |
221415 |
3.94 % |
| Transversion |
G>C |
Passed |
222258 |
3.95 % |
| |
|
|
|
|
| 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 |
3.10 |
36670453 |
11819037 |
| Passed |
2.24 |
3885097 |
1737078 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |