/EXTERNAL Roadmap/variants/K012819_1_lane_gembs
BACK
SAMPLE K012819_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165398563 |
823233629 |
70.64 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165398563 |
100% |
1130352144 |
96.99 % |
35046419 |
3.01 % |
| |
|
|
|
|
|
|
| Passed |
827475168 |
71.00 % |
819861825 |
72.53 % |
7613343 |
0.92 % |
| Filtered |
337923395 |
29.00 % |
310490319 |
27.47 % |
27433076 |
3.32 % |
| |
|
|
|
|
|
|
| q20 |
276422139 |
81.80 % |
272661451 |
87.82 % |
3760688 |
13.71 % |
| q20,qd2 |
35251658 |
10.43 % |
12539478 |
4.04 % |
22712180 |
82.79 % |
| q20,mq40 |
17405221 |
5.15 % |
17226083 |
5.55 % |
179138 |
0.65 % |
| q20,qd2,mq40 |
3972991 |
1.18 % |
3764333 |
1.21 % |
208658 |
0.76 % |
| qd2 |
2697019 |
0.80 % |
2438241 |
0.79 % |
258778 |
0.94 % |
| mq40 |
2140881 |
0.63 % |
1834866 |
0.59 % |
306015 |
1.12 % |
| qd2,mq40 |
32917 |
0.01 % |
25867 |
0.01 % |
7050 |
0.03 % |
| qd2,fs60,mq40 |
301 |
0.00 % |
0 |
0.00 % |
301 |
0.00 % |
| fs60,mq40 |
146 |
0.00 % |
0 |
0.00 % |
146 |
0.00 % |
| qd2,fs60 |
81 |
0.00 % |
0 |
0.00 % |
81 |
0.00 % |
| q20,qd2,fs60,mq40 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
13115292 |
35.93 % |
| Transition |
G>A |
All |
3114353 |
8.53 % |
| Transition |
T>C |
All |
9885043 |
27.08 % |
| Transition |
C>T |
All |
3016798 |
8.26 % |
| Transversion |
A>C |
All |
423788 |
1.16 % |
| Transversion |
C>A |
All |
1423840 |
3.90 % |
| Transversion |
T>G |
All |
550915 |
1.51 % |
| Transversion |
G>T |
All |
1375003 |
3.77 % |
| Transversion |
A>T |
All |
1292849 |
3.54 % |
| Transversion |
T>A |
All |
1334759 |
3.66 % |
| Transversion |
C>G |
All |
539784 |
1.48 % |
| Transversion |
G>C |
All |
430848 |
1.18 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
926414 |
22.85 % |
| Transition |
G>A |
Passed |
575354 |
14.19 % |
| Transition |
T>C |
Passed |
674618 |
16.64 % |
| Transition |
C>T |
Passed |
576561 |
14.22 % |
| Transversion |
A>C |
Passed |
156629 |
3.86 % |
| Transversion |
C>A |
Passed |
169200 |
4.17 % |
| Transversion |
T>G |
Passed |
165259 |
4.08 % |
| Transversion |
G>T |
Passed |
168440 |
4.16 % |
| Transversion |
A>T |
Passed |
159469 |
3.93 % |
| Transversion |
T>A |
Passed |
161553 |
3.99 % |
| Transversion |
C>G |
Passed |
162814 |
4.02 % |
| Transversion |
G>C |
Passed |
157191 |
3.88 % |
| |
|
|
|
|
| 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 |
3.95 |
29131486 |
7371786 |
| Passed |
2.12 |
2752947 |
1300555 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |