/EXTERNAL BLUEPRINT/variants/K006359_11_lane_gembs
BACK
SAMPLE K006359_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1107815444 |
637337786 |
57.53 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1107815444 |
100% |
1091618288 |
98.54 % |
16197156 |
1.46 % |
| |
|
|
|
|
|
|
| Passed |
638932593 |
57.68 % |
636015344 |
58.26 % |
2917249 |
0.46 % |
| Filtered |
468882851 |
42.32 % |
455602944 |
41.74 % |
13279907 |
2.08 % |
| |
|
|
|
|
|
|
| q20 |
396444926 |
84.55 % |
394862578 |
86.67 % |
1582348 |
11.92 % |
| q20,qd2 |
46925034 |
10.01 % |
35766066 |
7.85 % |
11158968 |
84.03 % |
| q20,mq40 |
14281758 |
3.05 % |
14181289 |
3.11 % |
100469 |
0.76 % |
| mq40 |
6344169 |
1.35 % |
6192714 |
1.36 % |
151455 |
1.14 % |
| q20,qd2,mq40 |
3198448 |
0.68 % |
3008048 |
0.66 % |
190400 |
1.43 % |
| qd2 |
1610641 |
0.34 % |
1531163 |
0.34 % |
79478 |
0.60 % |
| qd2,mq40 |
70975 |
0.02 % |
61086 |
0.01 % |
9889 |
0.07 % |
| q20,qd2,fs60 |
2437 |
0.00 % |
0 |
0.00 % |
2437 |
0.02 % |
| fs60 |
1433 |
0.00 % |
0 |
0.00 % |
1433 |
0.01 % |
| qd2,fs60,mq40 |
1116 |
0.00 % |
0 |
0.00 % |
1116 |
0.01 % |
| qd2,fs60 |
946 |
0.00 % |
0 |
0.00 % |
946 |
0.01 % |
| q20,qd2,fs60,mq40 |
533 |
0.00 % |
0 |
0.00 % |
533 |
0.00 % |
| fs60,mq40 |
432 |
0.00 % |
0 |
0.00 % |
432 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3034392 |
15.81 % |
| Transition |
G>A |
All |
5245748 |
27.33 % |
| Transition |
T>C |
All |
2885569 |
15.03 % |
| Transition |
C>T |
All |
5101584 |
26.57 % |
| Transversion |
A>C |
All |
238571 |
1.24 % |
| Transversion |
C>A |
All |
552162 |
2.88 % |
| Transversion |
T>G |
All |
256380 |
1.34 % |
| Transversion |
G>T |
All |
545061 |
2.84 % |
| Transversion |
A>T |
All |
469730 |
2.45 % |
| Transversion |
T>A |
All |
468130 |
2.44 % |
| Transversion |
C>G |
All |
204751 |
1.07 % |
| Transversion |
G>C |
All |
195446 |
1.02 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
369462 |
18.75 % |
| Transition |
G>A |
Passed |
338194 |
17.16 % |
| Transition |
T>C |
Passed |
368531 |
18.70 % |
| Transition |
C>T |
Passed |
337542 |
17.13 % |
| Transversion |
A>C |
Passed |
74194 |
3.77 % |
| Transversion |
C>A |
Passed |
67255 |
3.41 % |
| Transversion |
T>G |
Passed |
74346 |
3.77 % |
| Transversion |
G>T |
Passed |
67436 |
3.42 % |
| Transversion |
A>T |
Passed |
46516 |
2.36 % |
| Transversion |
T>A |
Passed |
46503 |
2.36 % |
| Transversion |
C>G |
Passed |
90086 |
4.57 % |
| Transversion |
G>C |
Passed |
90417 |
4.59 % |
| |
|
|
|
|
| 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 |
5.55 |
16267293 |
2930231 |
| Passed |
2.54 |
1413729 |
556753 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |