/cemt/variants/A59692_3_lane_gembs
BACK
SAMPLE A59692_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165584713 |
1047434278 |
89.86 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165584713 |
100% |
1152824854 |
98.91 % |
12759859 |
1.09 % |
| |
|
|
|
|
|
|
| Passed |
1048136701 |
89.92 % |
1044599096 |
90.61 % |
3537605 |
0.34 % |
| Filtered |
117448012 |
10.08 % |
108225758 |
9.39 % |
9222254 |
0.88 % |
| |
|
|
|
|
|
|
| q20 |
81393475 |
69.30 % |
80180039 |
74.09 % |
1213436 |
13.16 % |
| q20,qd2 |
12439535 |
10.59 % |
5587907 |
5.16 % |
6851628 |
74.29 % |
| q20,mq40 |
11423288 |
9.73 % |
11183182 |
10.33 % |
240106 |
2.60 % |
| qd2 |
5953907 |
5.07 % |
5579542 |
5.16 % |
374365 |
4.06 % |
| q20,qd2,mq40 |
3130667 |
2.67 % |
2832679 |
2.62 % |
297988 |
3.23 % |
| mq40 |
3023464 |
2.57 % |
2798605 |
2.59 % |
224859 |
2.44 % |
| qd2,mq40 |
75909 |
0.06 % |
63804 |
0.06 % |
12105 |
0.13 % |
| q20,qd2,fs60 |
2784 |
0.00 % |
0 |
0.00 % |
2784 |
0.03 % |
| fs60 |
1493 |
0.00 % |
0 |
0.00 % |
1493 |
0.02 % |
| qd2,fs60,mq40 |
1445 |
0.00 % |
0 |
0.00 % |
1445 |
0.02 % |
| qd2,fs60 |
1379 |
0.00 % |
0 |
0.00 % |
1379 |
0.01 % |
| fs60,mq40 |
540 |
0.00 % |
0 |
0.00 % |
540 |
0.01 % |
| q20,qd2,fs60,mq40 |
115 |
0.00 % |
0 |
0.00 % |
115 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
3617299 |
24.69 % |
| Transition |
G>A |
All |
1125063 |
7.68 % |
| Transition |
T>C |
All |
3613319 |
24.66 % |
| Transition |
C>T |
All |
1126067 |
7.69 % |
| Transversion |
A>C |
All |
466868 |
3.19 % |
| Transversion |
C>A |
All |
853095 |
5.82 % |
| Transversion |
T>G |
All |
461718 |
3.15 % |
| Transversion |
G>T |
All |
871639 |
5.95 % |
| Transversion |
A>T |
All |
944714 |
6.45 % |
| Transversion |
T>A |
All |
916655 |
6.26 % |
| Transversion |
C>G |
All |
324818 |
2.22 % |
| Transversion |
G>C |
All |
329384 |
2.25 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
687132 |
16.63 % |
| Transition |
G>A |
Passed |
610981 |
14.78 % |
| Transition |
T>C |
Passed |
688735 |
16.67 % |
| Transition |
C>T |
Passed |
611824 |
14.80 % |
| Transversion |
A>C |
Passed |
203295 |
4.92 % |
| Transversion |
C>A |
Passed |
214318 |
5.19 % |
| Transversion |
T>G |
Passed |
201631 |
4.88 % |
| Transversion |
G>T |
Passed |
212658 |
5.15 % |
| Transversion |
A>T |
Passed |
189073 |
4.57 % |
| Transversion |
T>A |
Passed |
189164 |
4.58 % |
| Transversion |
C>G |
Passed |
161603 |
3.91 % |
| Transversion |
G>C |
Passed |
162349 |
3.93 % |
| |
|
|
|
|
| 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 |
1.83 |
9481748 |
5168891 |
| Passed |
1.69 |
2598672 |
1534091 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |