/EXTERNAL Roadmap/variants/K012811_1_lane_gembs
BACK
SAMPLE K012811_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1126991478 |
20143024 |
1.79 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1126991478 |
100% |
1102347878 |
97.81 % |
24643600 |
2.19 % |
| |
|
|
|
|
|
|
| Passed |
30004507 |
2.66 % |
19565504 |
1.77 % |
10439003 |
34.79 % |
| Filtered |
1096986971 |
97.34 % |
1082782374 |
98.23 % |
14204597 |
47.34 % |
| |
|
|
|
|
|
|
| q20 |
1003015588 |
91.43 % |
995439944 |
91.93 % |
7575644 |
53.33 % |
| q20,qd2 |
66174623 |
6.03 % |
59897134 |
5.53 % |
6277489 |
44.19 % |
| q20,mq40 |
19138297 |
1.74 % |
19013279 |
1.76 % |
125018 |
0.88 % |
| q20,qd2,mq40 |
8385118 |
0.76 % |
8312353 |
0.77 % |
72765 |
0.51 % |
| mq40 |
250416 |
0.02 % |
100510 |
0.01 % |
149906 |
1.06 % |
| qd2 |
12933 |
0.00 % |
11399 |
0.00 % |
1534 |
0.01 % |
| qd2,mq40 |
9883 |
0.00 % |
7755 |
0.00 % |
2128 |
0.01 % |
| qd2,fs60,mq40 |
54 |
0.00 % |
0 |
0.00 % |
54 |
0.00 % |
| qd2,fs60 |
26 |
0.00 % |
0 |
0.00 % |
26 |
0.00 % |
| fs60,mq40 |
25 |
0.00 % |
0 |
0.00 % |
25 |
0.00 % |
| fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
8371870 |
30.67 % |
| Transition |
G>A |
All |
1252743 |
4.59 % |
| Transition |
T>C |
All |
4054089 |
14.85 % |
| Transition |
C>T |
All |
1368114 |
5.01 % |
| Transversion |
A>C |
All |
665480 |
2.44 % |
| Transversion |
C>A |
All |
2146145 |
7.86 % |
| Transversion |
T>G |
All |
1324649 |
4.85 % |
| Transversion |
G>T |
All |
1867959 |
6.84 % |
| Transversion |
A>T |
All |
2153509 |
7.89 % |
| Transversion |
T>A |
All |
2640792 |
9.67 % |
| Transversion |
C>G |
All |
924677 |
3.39 % |
| Transversion |
G>C |
All |
530055 |
1.94 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
102169 |
17.26 % |
| Transition |
G>A |
Passed |
64294 |
10.86 % |
| Transition |
T>C |
Passed |
73369 |
12.39 % |
| Transition |
C>T |
Passed |
69069 |
11.67 % |
| Transversion |
A>C |
Passed |
34154 |
5.77 % |
| Transversion |
C>A |
Passed |
36361 |
6.14 % |
| Transversion |
T>G |
Passed |
38573 |
6.52 % |
| Transversion |
G>T |
Passed |
36147 |
6.11 % |
| Transversion |
A>T |
Passed |
32299 |
5.46 % |
| Transversion |
T>A |
Passed |
32658 |
5.52 % |
| Transversion |
C>G |
Passed |
37848 |
6.39 % |
| Transversion |
G>C |
Passed |
35063 |
5.92 % |
| |
|
|
|
|
| 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 |
1.23 |
15046816 |
12253266 |
| Passed |
1.09 |
308901 |
283103 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |