/EXTERNAL Roadmap/variants/K012816_1_lane_gembs
BACK
SAMPLE K012816_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1163165165 |
1015119809 |
87.27 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1163165165 |
100% |
1144849259 |
98.43 % |
18315906 |
1.57 % |
| |
|
|
|
|
|
|
| Passed |
1016600803 |
87.40 % |
1012265745 |
88.42 % |
4335058 |
0.43 % |
| Filtered |
146564362 |
12.60 % |
132583514 |
11.58 % |
13980848 |
1.38 % |
| |
|
|
|
|
|
|
| q20 |
103248967 |
70.45 % |
101903912 |
76.86 % |
1345055 |
9.62 % |
| q20,qd2 |
17757085 |
12.12 % |
6133807 |
4.63 % |
11623278 |
83.14 % |
| q20,mq40 |
14323373 |
9.77 % |
14164087 |
10.68 % |
159286 |
1.14 % |
| mq40 |
4101311 |
2.80 % |
3815604 |
2.88 % |
285707 |
2.04 % |
| qd2 |
3714654 |
2.53 % |
3375930 |
2.55 % |
338724 |
2.42 % |
| q20,qd2,mq40 |
3359662 |
2.29 % |
3143654 |
2.37 % |
216008 |
1.55 % |
| qd2,mq40 |
57752 |
0.04 % |
46520 |
0.04 % |
11232 |
0.08 % |
| qd2,fs60,mq40 |
862 |
0.00 % |
0 |
0.00 % |
862 |
0.01 % |
| fs60,mq40 |
346 |
0.00 % |
0 |
0.00 % |
346 |
0.00 % |
| qd2,fs60 |
183 |
0.00 % |
0 |
0.00 % |
183 |
0.00 % |
| fs60 |
83 |
0.00 % |
0 |
0.00 % |
83 |
0.00 % |
| q20,qd2,fs60,mq40 |
73 |
0.00 % |
0 |
0.00 % |
73 |
0.00 % |
| q20,qd2,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
7919448 |
39.52 % |
| Transition |
G>A |
All |
1423476 |
7.10 % |
| Transition |
T>C |
All |
6050563 |
30.19 % |
| Transition |
C>T |
All |
1532272 |
7.65 % |
| Transversion |
A>C |
All |
245568 |
1.23 % |
| Transversion |
C>A |
All |
548910 |
2.74 % |
| Transversion |
T>G |
All |
289157 |
1.44 % |
| Transversion |
G>T |
All |
515090 |
2.57 % |
| Transversion |
A>T |
All |
482293 |
2.41 % |
| Transversion |
T>A |
All |
509666 |
2.54 % |
| Transversion |
C>G |
All |
278423 |
1.39 % |
| Transversion |
G>C |
All |
243823 |
1.22 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
858953 |
21.45 % |
| Transition |
G>A |
Passed |
602144 |
15.04 % |
| Transition |
T>C |
Passed |
705623 |
17.62 % |
| Transition |
C>T |
Passed |
611055 |
15.26 % |
| Transversion |
A>C |
Passed |
153812 |
3.84 % |
| Transversion |
C>A |
Passed |
160012 |
4.00 % |
| Transversion |
T>G |
Passed |
157002 |
3.92 % |
| Transversion |
G>T |
Passed |
160843 |
4.02 % |
| Transversion |
A>T |
Passed |
141193 |
3.53 % |
| Transversion |
T>A |
Passed |
141859 |
3.54 % |
| Transversion |
C>G |
Passed |
157161 |
3.92 % |
| Transversion |
G>C |
Passed |
154706 |
3.86 % |
| |
|
|
|
|
| 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 |
5.44 |
16925759 |
3112930 |
| Passed |
2.26 |
2777775 |
1226588 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |