/EXTERNAL Roadmap/variants/K006490_K006491_K006492_3_lane_gembs
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SAMPLE K006490_K006491_K006492_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156256803 |
1068776423 |
92.43 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156256803 |
100% |
1148788763 |
99.35 % |
7468040 |
0.65 % |
| |
|
|
|
|
|
|
| Passed |
1068972342 |
92.45 % |
1066022083 |
92.80 % |
2950259 |
0.28 % |
| Filtered |
87284461 |
7.55 % |
82766680 |
7.20 % |
4517781 |
0.42 % |
| |
|
|
|
|
|
|
| mq40 |
42655686 |
48.87 % |
42076480 |
50.84 % |
579206 |
12.82 % |
| q20,mq40 |
19010022 |
21.78 % |
18770180 |
22.68 % |
239842 |
5.31 % |
| q20 |
17272376 |
19.79 % |
16990751 |
20.53 % |
281625 |
6.23 % |
| q20,qd2 |
3196130 |
3.66 % |
842923 |
1.02 % |
2353207 |
52.09 % |
| q20,qd2,mq40 |
2520464 |
2.89 % |
1870556 |
2.26 % |
649908 |
14.39 % |
| qd2 |
2274725 |
2.61 % |
1990415 |
2.40 % |
284310 |
6.29 % |
| qd2,mq40 |
282951 |
0.32 % |
225375 |
0.27 % |
57576 |
1.27 % |
| q20,qd2,fs60 |
29046 |
0.03 % |
0 |
0.00 % |
29046 |
0.64 % |
| fs60 |
24973 |
0.03 % |
0 |
0.00 % |
24973 |
0.55 % |
| q20,fs60 |
7966 |
0.01 % |
0 |
0.00 % |
7966 |
0.18 % |
| fs60,mq40 |
7179 |
0.01 % |
0 |
0.00 % |
7179 |
0.16 % |
| qd2,fs60 |
1754 |
0.00 % |
0 |
0.00 % |
1754 |
0.04 % |
| q20,qd2,fs60,mq40 |
721 |
0.00 % |
0 |
0.00 % |
721 |
0.02 % |
| qd2,fs60,mq40 |
337 |
0.00 % |
0 |
0.00 % |
337 |
0.01 % |
| q20,fs60,mq40 |
131 |
0.00 % |
0 |
0.00 % |
131 |
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 |
2339805 |
26.01 % |
| Transition |
G>A |
All |
947056 |
10.53 % |
| Transition |
T>C |
All |
2355007 |
26.18 % |
| Transition |
C>T |
All |
961692 |
10.69 % |
| Transversion |
A>C |
All |
223907 |
2.49 % |
| Transversion |
C>A |
All |
384347 |
4.27 % |
| Transversion |
T>G |
All |
224145 |
2.49 % |
| Transversion |
G>T |
All |
387377 |
4.31 % |
| Transversion |
A>T |
All |
370932 |
4.12 % |
| Transversion |
T>A |
All |
364639 |
4.05 % |
| Transversion |
C>G |
All |
216300 |
2.40 % |
| Transversion |
G>C |
All |
219927 |
2.44 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
734964 |
18.46 % |
| Transition |
G>A |
Passed |
621402 |
15.60 % |
| Transition |
T>C |
Passed |
755035 |
18.96 % |
| Transition |
C>T |
Passed |
631786 |
15.86 % |
| Transversion |
A>C |
Passed |
159945 |
4.02 % |
| Transversion |
C>A |
Passed |
157195 |
3.95 % |
| Transversion |
T>G |
Passed |
159682 |
4.01 % |
| Transversion |
G>T |
Passed |
158678 |
3.98 % |
| Transversion |
A>T |
Passed |
143743 |
3.61 % |
| Transversion |
T>A |
Passed |
142598 |
3.58 % |
| Transversion |
C>G |
Passed |
157798 |
3.96 % |
| Transversion |
G>C |
Passed |
159493 |
4.01 % |
| |
|
|
|
|
| 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 |
2.76 |
6603560 |
2391574 |
| Passed |
2.21 |
2743187 |
1239132 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |