/EXTERNAL BLUEPRINT/variants/K006296_K006300_22_lane_gembs
BACK
SAMPLE K006296_K006300_22_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1115599513 |
669644149 |
60.03 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1115599513 |
100% |
1095649369 |
98.21 % |
19950144 |
1.79 % |
| |
|
|
|
|
|
|
| Passed |
671195712 |
60.16 % |
668330617 |
61.00 % |
2865095 |
0.43 % |
| Filtered |
444403801 |
39.84 % |
427318752 |
39.00 % |
17085049 |
2.55 % |
| |
|
|
|
|
|
|
| q20 |
353513841 |
79.55 % |
351616402 |
82.28 % |
1897439 |
11.11 % |
| q20,qd2 |
51705293 |
11.63 % |
37122399 |
8.69 % |
14582894 |
85.35 % |
| qd2 |
14951660 |
3.36 % |
14823875 |
3.47 % |
127785 |
0.75 % |
| q20,mq40 |
13051206 |
2.94 % |
12956118 |
3.03 % |
95088 |
0.56 % |
| mq40 |
8036774 |
1.81 % |
7871109 |
1.84 % |
165665 |
0.97 % |
| q20,qd2,mq40 |
3006888 |
0.68 % |
2823024 |
0.66 % |
183864 |
1.08 % |
| qd2,mq40 |
120454 |
0.03 % |
105825 |
0.02 % |
14629 |
0.09 % |
| q20,qd2,fs60 |
6330 |
0.00 % |
0 |
0.00 % |
6330 |
0.04 % |
| qd2,fs60 |
3620 |
0.00 % |
0 |
0.00 % |
3620 |
0.02 % |
| fs60 |
3599 |
0.00 % |
0 |
0.00 % |
3599 |
0.02 % |
| qd2,fs60,mq40 |
2481 |
0.00 % |
0 |
0.00 % |
2481 |
0.01 % |
| q20,qd2,fs60,mq40 |
843 |
0.00 % |
0 |
0.00 % |
843 |
0.00 % |
| fs60,mq40 |
805 |
0.00 % |
0 |
0.00 % |
805 |
0.00 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
3109679 |
8.67 % |
| Transition |
G>A |
All |
13634918 |
38.01 % |
| Transition |
T>C |
All |
2913578 |
8.12 % |
| Transition |
C>T |
All |
13529887 |
37.72 % |
| Transversion |
A>C |
All |
213168 |
0.59 % |
| Transversion |
C>A |
All |
531160 |
1.48 % |
| Transversion |
T>G |
All |
231257 |
0.64 % |
| Transversion |
G>T |
All |
518250 |
1.44 % |
| Transversion |
A>T |
All |
402580 |
1.12 % |
| Transversion |
T>A |
All |
398027 |
1.11 % |
| Transversion |
C>G |
All |
198639 |
0.55 % |
| Transversion |
G>C |
All |
187535 |
0.52 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
379888 |
18.85 % |
| Transition |
G>A |
Passed |
347077 |
17.22 % |
| Transition |
T>C |
Passed |
378320 |
18.77 % |
| Transition |
C>T |
Passed |
345600 |
17.15 % |
| Transversion |
A>C |
Passed |
74964 |
3.72 % |
| Transversion |
C>A |
Passed |
68467 |
3.40 % |
| Transversion |
T>G |
Passed |
74790 |
3.71 % |
| Transversion |
G>T |
Passed |
68272 |
3.39 % |
| Transversion |
A>T |
Passed |
48141 |
2.39 % |
| Transversion |
T>A |
Passed |
47832 |
2.37 % |
| Transversion |
C>G |
Passed |
90515 |
4.49 % |
| Transversion |
G>C |
Passed |
91182 |
4.53 % |
| |
|
|
|
|
| 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 |
12.38 |
33188062 |
2680616 |
| Passed |
2.57 |
1450885 |
564163 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |