/Martin Hirst/variants/PX0720_TTAGGC_10_lane_gembs
BACK
SAMPLE PX0720_TTAGGC_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1195310434 |
629711587 |
52.68 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1195310434 |
100% |
1117393434 |
93.48 % |
77917000 |
6.52 % |
| |
|
|
|
|
|
|
| Passed |
648206954 |
54.23 % |
624707628 |
55.91 % |
23499326 |
3.63 % |
| Filtered |
547103480 |
45.77 % |
492685806 |
44.09 % |
54417674 |
8.40 % |
| |
|
|
|
|
|
|
| q20 |
449898367 |
82.23 % |
432018416 |
87.69 % |
17879951 |
32.86 % |
| q20,qd2 |
70247404 |
12.84 % |
35202300 |
7.14 % |
35045104 |
64.40 % |
| qd2 |
12405713 |
2.27 % |
11581153 |
2.35 % |
824560 |
1.52 % |
| q20,mq40 |
9350870 |
1.71 % |
9121078 |
1.85 % |
229792 |
0.42 % |
| q20,qd2,mq40 |
4476700 |
0.82 % |
4305999 |
0.87 % |
170701 |
0.31 % |
| mq40 |
692146 |
0.13 % |
432352 |
0.09 % |
259794 |
0.48 % |
| qd2,mq40 |
32274 |
0.01 % |
24508 |
0.00 % |
7766 |
0.01 % |
| qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
18907074 |
23.35 % |
| Transition |
G>A |
All |
4444876 |
5.49 % |
| Transition |
T>C |
All |
18992435 |
23.45 % |
| Transition |
C>T |
All |
4515108 |
5.58 % |
| Transversion |
A>C |
All |
3508118 |
4.33 % |
| Transversion |
C>A |
All |
3981554 |
4.92 % |
| Transversion |
T>G |
All |
3386246 |
4.18 % |
| Transversion |
G>T |
All |
4082106 |
5.04 % |
| Transversion |
A>T |
All |
7722120 |
9.54 % |
| Transversion |
T>A |
All |
7561280 |
9.34 % |
| Transversion |
C>G |
All |
1910692 |
2.36 % |
| Transversion |
G>C |
All |
1969984 |
2.43 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1342436 |
24.45 % |
| Transition |
G>A |
Passed |
497391 |
9.06 % |
| Transition |
T>C |
Passed |
1402124 |
25.53 % |
| Transition |
C>T |
Passed |
511643 |
9.32 % |
| Transversion |
A>C |
Passed |
297962 |
5.43 % |
| Transversion |
C>A |
Passed |
159874 |
2.91 % |
| Transversion |
T>G |
Passed |
277129 |
5.05 % |
| Transversion |
G>T |
Passed |
166148 |
3.03 % |
| Transversion |
A>T |
Passed |
193014 |
3.51 % |
| Transversion |
T>A |
Passed |
181817 |
3.31 % |
| Transversion |
C>G |
Passed |
224732 |
4.09 % |
| Transversion |
G>C |
Passed |
237054 |
4.32 % |
| |
|
|
|
|
| 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 |
1.37 |
46859493 |
34122100 |
| Passed |
2.16 |
3753594 |
1737730 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |