/EXTERNAL Roadmap/variants/K012801_1_lane_gembs
BACK
SAMPLE K012801_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1159749628 |
762076100 |
65.71 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1159749628 |
100% |
1133672471 |
97.75 % |
26077157 |
2.25 % |
| |
|
|
|
|
|
|
| Passed |
765879194 |
66.04 % |
759068407 |
66.96 % |
6810787 |
0.89 % |
| Filtered |
393870434 |
33.96 % |
374604064 |
33.04 % |
19266370 |
2.52 % |
| |
|
|
|
|
|
|
| q20 |
346406185 |
87.95 % |
343175583 |
91.61 % |
3230602 |
16.77 % |
| q20,qd2 |
23514511 |
5.97 % |
8150420 |
2.18 % |
15364091 |
79.75 % |
| q20,mq40 |
16643654 |
4.23 % |
16493719 |
4.40 % |
149935 |
0.78 % |
| q20,qd2,mq40 |
3962681 |
1.01 % |
3800169 |
1.01 % |
162512 |
0.84 % |
| mq40 |
1957343 |
0.50 % |
1699602 |
0.45 % |
257741 |
1.34 % |
| qd2 |
1352272 |
0.34 % |
1258195 |
0.34 % |
94077 |
0.49 % |
| qd2,mq40 |
33074 |
0.01 % |
26376 |
0.01 % |
6698 |
0.03 % |
| qd2,fs60,mq40 |
413 |
0.00 % |
0 |
0.00 % |
413 |
0.00 % |
| fs60,mq40 |
136 |
0.00 % |
0 |
0.00 % |
136 |
0.00 % |
| qd2,fs60 |
109 |
0.00 % |
0 |
0.00 % |
109 |
0.00 % |
| q20,qd2,fs60,mq40 |
31 |
0.00 % |
0 |
0.00 % |
31 |
0.00 % |
| fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,qd2,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
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 |
10965537 |
39.38 % |
| Transition |
G>A |
All |
1749363 |
6.28 % |
| Transition |
T>C |
All |
8507924 |
30.55 % |
| Transition |
C>T |
All |
1926743 |
6.92 % |
| Transversion |
A>C |
All |
310078 |
1.11 % |
| Transversion |
C>A |
All |
887521 |
3.19 % |
| Transversion |
T>G |
All |
423504 |
1.52 % |
| Transversion |
G>T |
All |
814702 |
2.93 % |
| Transversion |
A>T |
All |
725980 |
2.61 % |
| Transversion |
T>A |
All |
798211 |
2.87 % |
| Transversion |
C>G |
All |
418373 |
1.50 % |
| Transversion |
G>C |
All |
318657 |
1.14 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
775157 |
20.09 % |
| Transition |
G>A |
Passed |
576183 |
14.93 % |
| Transition |
T>C |
Passed |
652327 |
16.90 % |
| Transition |
C>T |
Passed |
590333 |
15.30 % |
| Transversion |
A>C |
Passed |
156554 |
4.06 % |
| Transversion |
C>A |
Passed |
165999 |
4.30 % |
| Transversion |
T>G |
Passed |
160805 |
4.17 % |
| Transversion |
G>T |
Passed |
166959 |
4.33 % |
| Transversion |
A>T |
Passed |
147369 |
3.82 % |
| Transversion |
T>A |
Passed |
147521 |
3.82 % |
| Transversion |
C>G |
Passed |
161033 |
4.17 % |
| Transversion |
G>C |
Passed |
159114 |
4.12 % |
| |
|
|
|
|
| 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 |
4.93 |
23149567 |
4697026 |
| Passed |
2.05 |
2594000 |
1265354 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |