/cemt/variants/A75617_1_lane_gembs
BACK
SAMPLE A75617_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170005410 |
1036695169 |
88.61 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170005410 |
100% |
1152519791 |
98.51 % |
17485619 |
1.49 % |
| |
|
|
|
|
|
|
| Passed |
1038618280 |
88.77 % |
1033464221 |
89.67 % |
5154059 |
0.50 % |
| Filtered |
131387130 |
11.23 % |
119055570 |
10.33 % |
12331560 |
1.19 % |
| |
|
|
|
|
|
|
| q20 |
99122919 |
75.44 % |
98286797 |
82.56 % |
836122 |
6.78 % |
| q20,qd2 |
13719380 |
10.44 % |
3334775 |
2.80 % |
10384605 |
84.21 % |
| q20,mq40 |
10936684 |
8.32 % |
10816163 |
9.08 % |
120521 |
0.98 % |
| mq40 |
2784573 |
2.12 % |
2517417 |
2.11 % |
267156 |
2.17 % |
| q20,qd2,mq40 |
2598249 |
1.98 % |
2433718 |
2.04 % |
164531 |
1.33 % |
| qd2 |
2173412 |
1.65 % |
1626493 |
1.37 % |
546919 |
4.44 % |
| qd2,mq40 |
50339 |
0.04 % |
40207 |
0.03 % |
10132 |
0.08 % |
| qd2,fs60,mq40 |
709 |
0.00 % |
0 |
0.00 % |
709 |
0.01 % |
| qd2,fs60 |
305 |
0.00 % |
0 |
0.00 % |
305 |
0.00 % |
| fs60,mq40 |
263 |
0.00 % |
0 |
0.00 % |
263 |
0.00 % |
| fs60 |
179 |
0.00 % |
0 |
0.00 % |
179 |
0.00 % |
| q20,qd2,fs60,mq40 |
65 |
0.00 % |
0 |
0.00 % |
65 |
0.00 % |
| q20,qd2,fs60 |
48 |
0.00 % |
0 |
0.00 % |
48 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
7027914 |
36.63 % |
| Transition |
G>A |
All |
929067 |
4.84 % |
| Transition |
T>C |
All |
7083128 |
36.92 % |
| Transition |
C>T |
All |
935955 |
4.88 % |
| Transversion |
A>C |
All |
328924 |
1.71 % |
| Transversion |
C>A |
All |
489637 |
2.55 % |
| Transversion |
T>G |
All |
336421 |
1.75 % |
| Transversion |
G>T |
All |
472108 |
2.46 % |
| Transversion |
A>T |
All |
476325 |
2.48 % |
| Transversion |
T>A |
All |
496933 |
2.59 % |
| Transversion |
C>G |
All |
306079 |
1.60 % |
| Transversion |
G>C |
All |
302643 |
1.58 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
950393 |
21.42 % |
| Transition |
G>A |
Passed |
610682 |
13.76 % |
| Transition |
T>C |
Passed |
887167 |
20.00 % |
| Transition |
C>T |
Passed |
610985 |
13.77 % |
| Transversion |
A>C |
Passed |
179288 |
4.04 % |
| Transversion |
C>A |
Passed |
185471 |
4.18 % |
| Transversion |
T>G |
Passed |
182184 |
4.11 % |
| Transversion |
G>T |
Passed |
174708 |
3.94 % |
| Transversion |
A>T |
Passed |
154758 |
3.49 % |
| Transversion |
T>A |
Passed |
159707 |
3.60 % |
| Transversion |
C>G |
Passed |
171233 |
3.86 % |
| Transversion |
G>C |
Passed |
170298 |
3.84 % |
| |
|
|
|
|
| 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 |
4.98 |
15976064 |
3209070 |
| Passed |
2.22 |
3059227 |
1377647 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |