/EXTERNAL Roadmap/variants/K006538_K006539_2_lane_gembs
BACK
SAMPLE K006538_K006539_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1161645218 |
783852652 |
67.48 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1161645218 |
100% |
1136416360 |
97.83 % |
25228858 |
2.17 % |
| |
|
|
|
|
|
|
| Passed |
787660696 |
67.81 % |
781836859 |
68.80 % |
5823837 |
0.74 % |
| Filtered |
373984522 |
32.19 % |
354579501 |
31.20 % |
19405021 |
2.46 % |
| |
|
|
|
|
|
|
| q20 |
272020583 |
72.74 % |
265916682 |
74.99 % |
6103901 |
31.46 % |
| mq40 |
29257082 |
7.82 % |
28644774 |
8.08 % |
612308 |
3.16 % |
| q20,qd2 |
26610687 |
7.12 % |
15434478 |
4.35 % |
11176209 |
57.59 % |
| qd2 |
22505393 |
6.02 % |
22167212 |
6.25 % |
338181 |
1.74 % |
| q20,mq40 |
18889615 |
5.05 % |
18525281 |
5.22 % |
364334 |
1.88 % |
| q20,qd2,mq40 |
4072880 |
1.09 % |
3329125 |
0.94 % |
743755 |
3.83 % |
| qd2,mq40 |
612641 |
0.16 % |
561949 |
0.16 % |
50692 |
0.26 % |
| q20,qd2,fs60 |
4456 |
0.00 % |
0 |
0.00 % |
4456 |
0.02 % |
| qd2,fs60 |
4454 |
0.00 % |
0 |
0.00 % |
4454 |
0.02 % |
| fs60 |
2961 |
0.00 % |
0 |
0.00 % |
2961 |
0.02 % |
| qd2,fs60,mq40 |
2259 |
0.00 % |
0 |
0.00 % |
2259 |
0.01 % |
| fs60,mq40 |
844 |
0.00 % |
0 |
0.00 % |
844 |
0.00 % |
| q20,qd2,fs60,mq40 |
659 |
0.00 % |
0 |
0.00 % |
659 |
0.00 % |
| q20,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
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 |
6155532 |
18.87 % |
| Transition |
G>A |
All |
6229662 |
19.10 % |
| Transition |
T>C |
All |
9338330 |
28.63 % |
| Transition |
C>T |
All |
5671601 |
17.39 % |
| Transversion |
A>C |
All |
428647 |
1.31 % |
| Transversion |
C>A |
All |
768334 |
2.36 % |
| Transversion |
T>G |
All |
479848 |
1.47 % |
| Transversion |
G>T |
All |
775681 |
2.38 % |
| Transversion |
A>T |
All |
1091987 |
3.35 % |
| Transversion |
T>A |
All |
1047214 |
3.21 % |
| Transversion |
C>G |
All |
328818 |
1.01 % |
| Transversion |
G>C |
All |
304227 |
0.93 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
560519 |
19.96 % |
| Transition |
G>A |
Passed |
421066 |
14.99 % |
| Transition |
T>C |
Passed |
617766 |
22.00 % |
| Transition |
C>T |
Passed |
418094 |
14.89 % |
| Transversion |
A>C |
Passed |
105873 |
3.77 % |
| Transversion |
C>A |
Passed |
95400 |
3.40 % |
| Transversion |
T>G |
Passed |
106815 |
3.80 % |
| Transversion |
G>T |
Passed |
95408 |
3.40 % |
| Transversion |
A>T |
Passed |
76938 |
2.74 % |
| Transversion |
T>A |
Passed |
77200 |
2.75 % |
| Transversion |
C>G |
Passed |
116718 |
4.16 % |
| Transversion |
G>C |
Passed |
116617 |
4.15 % |
| |
|
|
|
|
| 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 |
5.24 |
27395125 |
5224756 |
| Passed |
2.55 |
2017445 |
790969 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |