/EXTERNAL BLUEPRINT/variants/K006348_9_lane_gembs
BACK
SAMPLE K006348_9_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1104529354 |
598841098 |
54.22 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1104529354 |
100% |
1088035717 |
98.51 % |
16493637 |
1.49 % |
| |
|
|
|
|
|
|
| Passed |
600676556 |
54.38 % |
597609324 |
54.93 % |
3067232 |
0.51 % |
| Filtered |
503852798 |
45.62 % |
490426393 |
45.07 % |
13426405 |
2.24 % |
| |
|
|
|
|
|
|
| q20 |
425031865 |
84.36 % |
423481380 |
86.35 % |
1550485 |
11.55 % |
| q20,qd2 |
51944409 |
10.31 % |
40627898 |
8.28 % |
11316511 |
84.29 % |
| q20,mq40 |
15346093 |
3.05 % |
15241392 |
3.11 % |
104701 |
0.78 % |
| mq40 |
6425022 |
1.28 % |
6266289 |
1.28 % |
158733 |
1.18 % |
| q20,qd2,mq40 |
3387034 |
0.67 % |
3187436 |
0.65 % |
199598 |
1.49 % |
| qd2 |
1637052 |
0.32 % |
1557281 |
0.32 % |
79771 |
0.59 % |
| qd2,mq40 |
74785 |
0.01 % |
64717 |
0.01 % |
10068 |
0.07 % |
| q20,qd2,fs60 |
2397 |
0.00 % |
0 |
0.00 % |
2397 |
0.02 % |
| fs60 |
1341 |
0.00 % |
0 |
0.00 % |
1341 |
0.01 % |
| qd2,fs60,mq40 |
964 |
0.00 % |
0 |
0.00 % |
964 |
0.01 % |
| qd2,fs60 |
904 |
0.00 % |
0 |
0.00 % |
904 |
0.01 % |
| q20,qd2,fs60,mq40 |
529 |
0.00 % |
0 |
0.00 % |
529 |
0.00 % |
| fs60,mq40 |
403 |
0.00 % |
0 |
0.00 % |
403 |
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 |
3261898 |
16.52 % |
| Transition |
G>A |
All |
5339918 |
27.05 % |
| Transition |
T>C |
All |
3123647 |
15.82 % |
| Transition |
C>T |
All |
5200910 |
26.35 % |
| Transversion |
A>C |
All |
206010 |
1.04 % |
| Transversion |
C>A |
All |
565945 |
2.87 % |
| Transversion |
T>G |
All |
217781 |
1.10 % |
| Transversion |
G>T |
All |
561278 |
2.84 % |
| Transversion |
A>T |
All |
448748 |
2.27 % |
| Transversion |
T>A |
All |
447951 |
2.27 % |
| Transversion |
C>G |
All |
187512 |
0.95 % |
| Transversion |
G>C |
All |
179212 |
0.91 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
348700 |
19.00 % |
| Transition |
G>A |
Passed |
312808 |
17.04 % |
| Transition |
T>C |
Passed |
348232 |
18.97 % |
| Transition |
C>T |
Passed |
313072 |
17.06 % |
| Transversion |
A>C |
Passed |
68647 |
3.74 % |
| Transversion |
C>A |
Passed |
61858 |
3.37 % |
| Transversion |
T>G |
Passed |
68533 |
3.73 % |
| Transversion |
G>T |
Passed |
61787 |
3.37 % |
| Transversion |
A>T |
Passed |
41973 |
2.29 % |
| Transversion |
T>A |
Passed |
41915 |
2.28 % |
| Transversion |
C>G |
Passed |
83654 |
4.56 % |
| Transversion |
G>C |
Passed |
84036 |
4.58 % |
| |
|
|
|
|
| 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 |
6.01 |
16926373 |
2814437 |
| Passed |
2.58 |
1322812 |
512403 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |