/EXTERNAL Roadmap/variants/K012805_1_lane_gembs
BACK
SAMPLE K012805_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157355901 |
1017967823 |
87.96 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157355901 |
100% |
1139395107 |
98.45 % |
17960794 |
1.55 % |
| |
|
|
|
|
|
|
| Passed |
1019204408 |
88.06 % |
1014598125 |
89.05 % |
4606283 |
0.45 % |
| Filtered |
138151493 |
11.94 % |
124796982 |
10.95 % |
13354511 |
1.31 % |
| |
|
|
|
|
|
|
| q20 |
95998788 |
69.49 % |
94817208 |
75.98 % |
1181580 |
8.85 % |
| q20,qd2 |
16825896 |
12.18 % |
5622818 |
4.51 % |
11203078 |
83.89 % |
| q20,mq40 |
14775847 |
10.70 % |
14620910 |
11.72 % |
154937 |
1.16 % |
| mq40 |
4171271 |
3.02 % |
3891355 |
3.12 % |
279916 |
2.10 % |
| q20,qd2,mq40 |
3400295 |
2.46 % |
3193124 |
2.56 % |
207171 |
1.55 % |
| qd2 |
2931911 |
2.12 % |
2614503 |
2.10 % |
317408 |
2.38 % |
| qd2,mq40 |
46479 |
0.03 % |
37064 |
0.03 % |
9415 |
0.07 % |
| qd2,fs60,mq40 |
521 |
0.00 % |
0 |
0.00 % |
521 |
0.00 % |
| fs60,mq40 |
237 |
0.00 % |
0 |
0.00 % |
237 |
0.00 % |
| qd2,fs60 |
158 |
0.00 % |
0 |
0.00 % |
158 |
0.00 % |
| fs60 |
47 |
0.00 % |
0 |
0.00 % |
47 |
0.00 % |
| q20,qd2,fs60,mq40 |
38 |
0.00 % |
0 |
0.00 % |
38 |
0.00 % |
| q20,qd2,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
7358573 |
38.14 % |
| Transition |
G>A |
All |
1400699 |
7.26 % |
| Transition |
T>C |
All |
5879431 |
30.48 % |
| Transition |
C>T |
All |
1549510 |
8.03 % |
| Transversion |
A>C |
All |
257192 |
1.33 % |
| Transversion |
C>A |
All |
532884 |
2.76 % |
| Transversion |
T>G |
All |
288773 |
1.50 % |
| Transversion |
G>T |
All |
510680 |
2.65 % |
| Transversion |
A>T |
All |
486000 |
2.52 % |
| Transversion |
T>A |
All |
501484 |
2.60 % |
| Transversion |
C>G |
All |
276127 |
1.43 % |
| Transversion |
G>C |
All |
250750 |
1.30 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
840087 |
20.02 % |
| Transition |
G>A |
Passed |
642625 |
15.31 % |
| Transition |
T>C |
Passed |
717944 |
17.11 % |
| Transition |
C>T |
Passed |
651518 |
15.53 % |
| Transversion |
A>C |
Passed |
168102 |
4.01 % |
| Transversion |
C>A |
Passed |
177360 |
4.23 % |
| Transversion |
T>G |
Passed |
170668 |
4.07 % |
| Transversion |
G>T |
Passed |
177409 |
4.23 % |
| Transversion |
A>T |
Passed |
155562 |
3.71 % |
| Transversion |
T>A |
Passed |
155329 |
3.70 % |
| Transversion |
C>G |
Passed |
170500 |
4.06 % |
| Transversion |
G>C |
Passed |
169113 |
4.03 % |
| |
|
|
|
|
| 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 |
5.22 |
16188213 |
3103890 |
| Passed |
2.12 |
2852174 |
1344043 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |