/EXTERNAL DEEP/variants/K008982_K008983_K008984_K008985_K008986_4_lane_gembs
BACK
SAMPLE K008982_K008983_K008984_K008985_K008986_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1136333407 |
130137088 |
11.45 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1136333407 |
100% |
1105349118 |
97.27 % |
30984289 |
2.73 % |
| |
|
|
|
|
|
|
| Passed |
141376831 |
12.44 % |
128014012 |
11.58 % |
13362819 |
9.45 % |
| Filtered |
994956576 |
87.56 % |
977335106 |
88.42 % |
17621470 |
12.46 % |
| |
|
|
|
|
|
|
| q20 |
910504510 |
91.51 % |
903287115 |
92.42 % |
7217395 |
40.96 % |
| q20,mq40 |
39561883 |
3.98 % |
39101538 |
4.00 % |
460345 |
2.61 % |
| q20,qd2 |
33740955 |
3.39 % |
24914123 |
2.55 % |
8826832 |
50.09 % |
| q20,qd2,mq40 |
9689792 |
0.97 % |
9383294 |
0.96 % |
306498 |
1.74 % |
| mq40 |
1400754 |
0.14 % |
598707 |
0.06 % |
802047 |
4.55 % |
| qd2 |
44545 |
0.00 % |
39966 |
0.00 % |
4579 |
0.03 % |
| qd2,mq40 |
14010 |
0.00 % |
10363 |
0.00 % |
3647 |
0.02 % |
| fs60,mq40 |
41 |
0.00 % |
0 |
0.00 % |
41 |
0.00 % |
| qd2,fs60,mq40 |
32 |
0.00 % |
0 |
0.00 % |
32 |
0.00 % |
| qd2,fs60 |
31 |
0.00 % |
0 |
0.00 % |
31 |
0.00 % |
| fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
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 |
7835787 |
23.68 % |
| Transition |
G>A |
All |
1750856 |
5.29 % |
| Transition |
T>C |
All |
7742883 |
23.40 % |
| Transition |
C>T |
All |
1692398 |
5.11 % |
| Transversion |
A>C |
All |
899371 |
2.72 % |
| Transversion |
C>A |
All |
3657826 |
11.05 % |
| Transversion |
T>G |
All |
909551 |
2.75 % |
| Transversion |
G>T |
All |
3556818 |
10.75 % |
| Transversion |
A>T |
All |
1880836 |
5.68 % |
| Transversion |
T>A |
All |
1949778 |
5.89 % |
| Transversion |
C>G |
All |
621480 |
1.88 % |
| Transversion |
G>C |
All |
598654 |
1.81 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
451490 |
20.80 % |
| Transition |
G>A |
Passed |
195939 |
9.03 % |
| Transition |
T>C |
Passed |
446303 |
20.56 % |
| Transition |
C>T |
Passed |
196816 |
9.07 % |
| Transversion |
A>C |
Passed |
84037 |
3.87 % |
| Transversion |
C>A |
Passed |
186073 |
8.57 % |
| Transversion |
T>G |
Passed |
86296 |
3.98 % |
| Transversion |
G>T |
Passed |
185774 |
8.56 % |
| Transversion |
A>T |
Passed |
75528 |
3.48 % |
| Transversion |
T>A |
Passed |
80508 |
3.71 % |
| Transversion |
C>G |
Passed |
91865 |
4.23 % |
| Transversion |
G>C |
Passed |
89965 |
4.14 % |
| |
|
|
|
|
| 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 |
1.35 |
19021924 |
14074314 |
| Passed |
1.47 |
1290548 |
880046 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |