/CEMT/variants/A75621_1_lane_gembs
BACK
SAMPLE A75621_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1176944553 |
915158437 |
77.76 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1176944553 |
100% |
1157670993 |
98.36 % |
19273560 |
1.64 % |
| |
|
|
|
|
|
|
| Passed |
918620182 |
78.05 % |
912187969 |
78.80 % |
6432213 |
0.70 % |
| Filtered |
258324371 |
21.95 % |
245483024 |
21.20 % |
12841347 |
1.40 % |
| |
|
|
|
|
|
|
| q20 |
224726588 |
86.99 % |
223139171 |
90.90 % |
1587417 |
12.36 % |
| q20,qd2 |
14485598 |
5.61 % |
4168842 |
1.70 % |
10316756 |
80.34 % |
| q20,mq40 |
11721697 |
4.54 % |
11590026 |
4.72 % |
131671 |
1.03 % |
| q20,qd2,mq40 |
2799654 |
1.08 % |
2638678 |
1.07 % |
160976 |
1.25 % |
| mq40 |
2547489 |
0.99 % |
2287692 |
0.93 % |
259797 |
2.02 % |
| qd2 |
1992852 |
0.77 % |
1618924 |
0.66 % |
373928 |
2.91 % |
| qd2,mq40 |
48619 |
0.02 % |
39691 |
0.02 % |
8928 |
0.07 % |
| qd2,fs60,mq40 |
865 |
0.00 % |
0 |
0.00 % |
865 |
0.01 % |
| qd2,fs60 |
358 |
0.00 % |
0 |
0.00 % |
358 |
0.00 % |
| fs60,mq40 |
250 |
0.00 % |
0 |
0.00 % |
250 |
0.00 % |
| fs60 |
212 |
0.00 % |
0 |
0.00 % |
212 |
0.00 % |
| q20,qd2,fs60 |
107 |
0.00 % |
0 |
0.00 % |
107 |
0.00 % |
| q20,qd2,fs60,mq40 |
81 |
0.00 % |
0 |
0.00 % |
81 |
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 |
7760976 |
36.88 % |
| Transition |
G>A |
All |
929016 |
4.42 % |
| Transition |
T>C |
All |
7790501 |
37.02 % |
| Transition |
C>T |
All |
930462 |
4.42 % |
| Transversion |
A>C |
All |
405682 |
1.93 % |
| Transversion |
C>A |
All |
534311 |
2.54 % |
| Transversion |
T>G |
All |
410918 |
1.95 % |
| Transversion |
G>T |
All |
522338 |
2.48 % |
| Transversion |
A>T |
All |
480692 |
2.28 % |
| Transversion |
T>A |
All |
490970 |
2.33 % |
| Transversion |
C>G |
All |
393549 |
1.87 % |
| Transversion |
G>C |
All |
392231 |
1.86 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
863609 |
21.30 % |
| Transition |
G>A |
Passed |
553774 |
13.66 % |
| Transition |
T>C |
Passed |
791967 |
19.54 % |
| Transition |
C>T |
Passed |
553510 |
13.65 % |
| Transversion |
A>C |
Passed |
167250 |
4.13 % |
| Transversion |
C>A |
Passed |
174640 |
4.31 % |
| Transversion |
T>G |
Passed |
169878 |
4.19 % |
| Transversion |
G>T |
Passed |
164863 |
4.07 % |
| Transversion |
A>T |
Passed |
145562 |
3.59 % |
| Transversion |
T>A |
Passed |
150074 |
3.70 % |
| Transversion |
C>G |
Passed |
159858 |
3.94 % |
| Transversion |
G>C |
Passed |
159014 |
3.92 % |
| |
|
|
|
|
| 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 |
4.80 |
17410955 |
3630691 |
| Passed |
2.14 |
2762860 |
1291139 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |