/cemt/variants/A36006_3_lane_gembs
BACK
SAMPLE A36006_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1160383055 |
732879010 |
63.16 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1160383055 |
100% |
1140052660 |
98.25 % |
20330395 |
1.75 % |
| |
|
|
|
|
|
|
| Passed |
735745064 |
63.41 % |
730517828 |
64.08 % |
5227236 |
0.71 % |
| Filtered |
424637991 |
36.59 % |
409534832 |
35.92 % |
15103159 |
2.05 % |
| |
|
|
|
|
|
|
| q20 |
380586141 |
89.63 % |
376863046 |
92.02 % |
3723095 |
24.65 % |
| q20,qd2 |
23082855 |
5.44 % |
12491089 |
3.05 % |
10591766 |
70.13 % |
| q20,mq40 |
11417442 |
2.69 % |
11197877 |
2.73 % |
219565 |
1.45 % |
| qd2 |
4460786 |
1.05 % |
4293150 |
1.05 % |
167636 |
1.11 % |
| q20,qd2,mq40 |
3382966 |
0.80 % |
3159699 |
0.77 % |
223267 |
1.48 % |
| mq40 |
1649206 |
0.39 % |
1484278 |
0.36 % |
164928 |
1.09 % |
| qd2,mq40 |
54810 |
0.01 % |
45693 |
0.01 % |
9117 |
0.06 % |
| qd2,fs60,mq40 |
998 |
0.00 % |
0 |
0.00 % |
998 |
0.01 % |
| fs60 |
877 |
0.00 % |
0 |
0.00 % |
877 |
0.01 % |
| qd2,fs60 |
756 |
0.00 % |
0 |
0.00 % |
756 |
0.01 % |
| q20,qd2,fs60 |
707 |
0.00 % |
0 |
0.00 % |
707 |
0.00 % |
| fs60,mq40 |
300 |
0.00 % |
0 |
0.00 % |
300 |
0.00 % |
| q20,qd2,fs60,mq40 |
140 |
0.00 % |
0 |
0.00 % |
140 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
6375065 |
28.56 % |
| Transition |
G>A |
All |
1700722 |
7.62 % |
| Transition |
T>C |
All |
6224022 |
27.89 % |
| Transition |
C>T |
All |
1719774 |
7.71 % |
| Transversion |
A>C |
All |
467376 |
2.09 % |
| Transversion |
C>A |
All |
1181825 |
5.30 % |
| Transversion |
T>G |
All |
472340 |
2.12 % |
| Transversion |
G>T |
All |
1183856 |
5.30 % |
| Transversion |
A>T |
All |
1095824 |
4.91 % |
| Transversion |
T>A |
All |
1096380 |
4.91 % |
| Transversion |
C>G |
All |
404771 |
1.81 % |
| Transversion |
G>C |
All |
397247 |
1.78 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
563547 |
17.53 % |
| Transition |
G>A |
Passed |
502126 |
15.62 % |
| Transition |
T>C |
Passed |
563934 |
17.54 % |
| Transition |
C>T |
Passed |
503476 |
15.66 % |
| Transversion |
A>C |
Passed |
135548 |
4.22 % |
| Transversion |
C>A |
Passed |
145562 |
4.53 % |
| Transversion |
T>G |
Passed |
135662 |
4.22 % |
| Transversion |
G>T |
Passed |
144416 |
4.49 % |
| Transversion |
A>T |
Passed |
133372 |
4.15 % |
| Transversion |
T>A |
Passed |
133643 |
4.16 % |
| Transversion |
C>G |
Passed |
126754 |
3.94 % |
| Transversion |
G>C |
Passed |
126507 |
3.94 % |
| |
|
|
|
|
| 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 |
2.54 |
16019583 |
6299619 |
| Passed |
1.97 |
2133083 |
1081464 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |