/EXTERNAL DEEP/variants/K009043_K009044_K009045_3_lane_gembs
BACK
SAMPLE K009043_K009044_K009045_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1169701077 |
837078930 |
71.56 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1169701077 |
100% |
1137366459 |
97.24 % |
32334618 |
2.76 % |
| |
|
|
|
|
|
|
| Passed |
841723695 |
71.96 % |
833052825 |
73.24 % |
8670870 |
1.03 % |
| Filtered |
327977382 |
28.04 % |
304313634 |
26.76 % |
23663748 |
2.81 % |
| |
|
|
|
|
|
|
| q20 |
284161063 |
86.64 % |
277486439 |
91.18 % |
6674624 |
28.21 % |
| q20,qd2 |
25638420 |
7.82 % |
9582191 |
3.15 % |
16056229 |
67.85 % |
| q20,mq40 |
8833899 |
2.69 % |
8675394 |
2.85 % |
158505 |
0.67 % |
| qd2 |
5261319 |
1.60 % |
4871363 |
1.60 % |
389956 |
1.65 % |
| q20,qd2,mq40 |
2882384 |
0.88 % |
2730817 |
0.90 % |
151567 |
0.64 % |
| mq40 |
1149710 |
0.35 % |
928537 |
0.31 % |
221173 |
0.93 % |
| qd2,mq40 |
47730 |
0.01 % |
38893 |
0.01 % |
8837 |
0.04 % |
| qd2,fs60,mq40 |
794 |
0.00 % |
0 |
0.00 % |
794 |
0.00 % |
| fs60 |
617 |
0.00 % |
0 |
0.00 % |
617 |
0.00 % |
| qd2,fs60 |
596 |
0.00 % |
0 |
0.00 % |
596 |
0.00 % |
| q20,qd2,fs60 |
374 |
0.00 % |
0 |
0.00 % |
374 |
0.00 % |
| fs60,mq40 |
310 |
0.00 % |
0 |
0.00 % |
310 |
0.00 % |
| q20,qd2,fs60,mq40 |
164 |
0.00 % |
0 |
0.00 % |
164 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
11696223 |
34.15 % |
| Transition |
G>A |
All |
2643874 |
7.72 % |
| Transition |
T>C |
All |
13621955 |
39.77 % |
| Transition |
C>T |
All |
2003680 |
5.85 % |
| Transversion |
A>C |
All |
312809 |
0.91 % |
| Transversion |
C>A |
All |
883101 |
2.58 % |
| Transversion |
T>G |
All |
373299 |
1.09 % |
| Transversion |
G>T |
All |
832012 |
2.43 % |
| Transversion |
A>T |
All |
589964 |
1.72 % |
| Transversion |
T>A |
All |
638914 |
1.87 % |
| Transversion |
C>G |
All |
334152 |
0.98 % |
| Transversion |
G>C |
All |
317900 |
0.93 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
989848 |
20.07 % |
| Transition |
G>A |
Passed |
596558 |
12.09 % |
| Transition |
T>C |
Passed |
1622580 |
32.89 % |
| Transition |
C>T |
Passed |
541416 |
10.97 % |
| Transversion |
A>C |
Passed |
142854 |
2.90 % |
| Transversion |
C>A |
Passed |
170807 |
3.46 % |
| Transversion |
T>G |
Passed |
153562 |
3.11 % |
| Transversion |
G>T |
Passed |
160314 |
3.25 % |
| Transversion |
A>T |
Passed |
126255 |
2.56 % |
| Transversion |
T>A |
Passed |
138720 |
2.81 % |
| Transversion |
C>G |
Passed |
146219 |
2.96 % |
| Transversion |
G>C |
Passed |
144062 |
2.92 % |
| |
|
|
|
|
| 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 |
7.00 |
29965732 |
4282151 |
| Passed |
3.17 |
3750402 |
1182793 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |