/CEMT/variants/B35054_1_lane_gembs
BACK
SAMPLE B35054_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1169447272 |
1003893488 |
85.84 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1169447272 |
100% |
1151854004 |
98.50 % |
17593268 |
1.50 % |
| |
|
|
|
|
|
|
| Passed |
1006304496 |
86.05 % |
1000830640 |
86.89 % |
5473856 |
0.54 % |
| Filtered |
163142776 |
13.95 % |
151023364 |
13.11 % |
12119412 |
1.20 % |
| |
|
|
|
|
|
|
| q20 |
132779857 |
81.39 % |
131780937 |
87.26 % |
998920 |
8.24 % |
| q20,qd2 |
13871614 |
8.50 % |
3557149 |
2.36 % |
10314465 |
85.11 % |
| q20,mq40 |
9622315 |
5.90 % |
9521317 |
6.30 % |
100998 |
0.83 % |
| q20,qd2,mq40 |
2442376 |
1.50 % |
2304839 |
1.53 % |
137537 |
1.13 % |
| mq40 |
2253527 |
1.38 % |
2019056 |
1.34 % |
234471 |
1.93 % |
| qd2 |
2118071 |
1.30 % |
1797262 |
1.19 % |
320809 |
2.65 % |
| qd2,mq40 |
52632 |
0.03 % |
42804 |
0.03 % |
9828 |
0.08 % |
| qd2,fs60,mq40 |
916 |
0.00 % |
0 |
0.00 % |
916 |
0.01 % |
| qd2,fs60 |
612 |
0.00 % |
0 |
0.00 % |
612 |
0.01 % |
| fs60 |
375 |
0.00 % |
0 |
0.00 % |
375 |
0.00 % |
| fs60,mq40 |
274 |
0.00 % |
0 |
0.00 % |
274 |
0.00 % |
| q20,qd2,fs60 |
138 |
0.00 % |
0 |
0.00 % |
138 |
0.00 % |
| q20,qd2,fs60,mq40 |
68 |
0.00 % |
0 |
0.00 % |
68 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
7151802 |
37.10 % |
| Transition |
G>A |
All |
997235 |
5.17 % |
| Transition |
T>C |
All |
7123846 |
36.96 % |
| Transition |
C>T |
All |
1000811 |
5.19 % |
| Transversion |
A>C |
All |
359990 |
1.87 % |
| Transversion |
C>A |
All |
434958 |
2.26 % |
| Transversion |
T>G |
All |
362103 |
1.88 % |
| Transversion |
G>T |
All |
427357 |
2.22 % |
| Transversion |
A>T |
All |
390741 |
2.03 % |
| Transversion |
T>A |
All |
396025 |
2.05 % |
| Transversion |
C>G |
All |
316765 |
1.64 % |
| Transversion |
G>C |
All |
314473 |
1.63 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
799138 |
18.87 % |
| Transition |
G>A |
Passed |
620183 |
14.65 % |
| Transition |
T>C |
Passed |
799952 |
18.89 % |
| Transition |
C>T |
Passed |
620009 |
14.64 % |
| Transversion |
A>C |
Passed |
184906 |
4.37 % |
| Transversion |
C>A |
Passed |
187319 |
4.42 % |
| Transversion |
T>G |
Passed |
185117 |
4.37 % |
| Transversion |
G>T |
Passed |
179552 |
4.24 % |
| Transversion |
A>T |
Passed |
157810 |
3.73 % |
| Transversion |
T>A |
Passed |
160768 |
3.80 % |
| Transversion |
C>G |
Passed |
169543 |
4.00 % |
| Transversion |
G>C |
Passed |
170134 |
4.02 % |
| |
|
|
|
|
| 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 |
5.42 |
16273694 |
3002412 |
| Passed |
2.04 |
2839282 |
1395149 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |