/EXTERNAL BLUEPRINT/variants/K006354_12_lane_gembs
BACK
SAMPLE K006354_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1109082726 |
634551486 |
57.21 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1109082726 |
100% |
1095100480 |
98.74 % |
13982246 |
1.26 % |
| |
|
|
|
|
|
|
| Passed |
636178700 |
57.36 % |
633197083 |
57.82 % |
2981617 |
0.47 % |
| Filtered |
472904026 |
42.64 % |
461903397 |
42.18 % |
11000629 |
1.73 % |
| |
|
|
|
|
|
|
| q20 |
404854069 |
85.61 % |
403423782 |
87.34 % |
1430287 |
13.00 % |
| q20,qd2 |
43163869 |
9.13 % |
34130574 |
7.39 % |
9033295 |
82.12 % |
| q20,mq40 |
14114241 |
2.98 % |
14011015 |
3.03 % |
103226 |
0.94 % |
| mq40 |
5427480 |
1.15 % |
5273464 |
1.14 % |
154016 |
1.40 % |
| q20,qd2,mq40 |
3290045 |
0.70 % |
3103361 |
0.67 % |
186684 |
1.70 % |
| qd2 |
1976240 |
0.42 % |
1899164 |
0.41 % |
77076 |
0.70 % |
| qd2,mq40 |
72377 |
0.02 % |
62037 |
0.01 % |
10340 |
0.09 % |
| q20,qd2,fs60 |
1758 |
0.00 % |
0 |
0.00 % |
1758 |
0.02 % |
| fs60 |
1189 |
0.00 % |
0 |
0.00 % |
1189 |
0.01 % |
| qd2,fs60,mq40 |
1073 |
0.00 % |
0 |
0.00 % |
1073 |
0.01 % |
| qd2,fs60 |
723 |
0.00 % |
0 |
0.00 % |
723 |
0.01 % |
| fs60,mq40 |
485 |
0.00 % |
0 |
0.00 % |
485 |
0.00 % |
| q20,qd2,fs60,mq40 |
470 |
0.00 % |
0 |
0.00 % |
470 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60 |
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 |
2954566 |
18.35 % |
| Transition |
G>A |
All |
3691251 |
22.92 % |
| Transition |
T>C |
All |
2873042 |
17.84 % |
| Transition |
C>T |
All |
3625330 |
22.51 % |
| Transversion |
A>C |
All |
213590 |
1.33 % |
| Transversion |
C>A |
All |
625788 |
3.89 % |
| Transversion |
T>G |
All |
220371 |
1.37 % |
| Transversion |
G>T |
All |
624961 |
3.88 % |
| Transversion |
A>T |
All |
458909 |
2.85 % |
| Transversion |
T>A |
All |
445184 |
2.76 % |
| Transversion |
C>G |
All |
187153 |
1.16 % |
| Transversion |
G>C |
All |
181916 |
1.13 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
367537 |
18.44 % |
| Transition |
G>A |
Passed |
343627 |
17.24 % |
| Transition |
T>C |
Passed |
366439 |
18.38 % |
| Transition |
C>T |
Passed |
344009 |
17.26 % |
| Transversion |
A>C |
Passed |
76483 |
3.84 % |
| Transversion |
C>A |
Passed |
70774 |
3.55 % |
| Transversion |
T>G |
Passed |
75614 |
3.79 % |
| Transversion |
G>T |
Passed |
71098 |
3.57 % |
| Transversion |
A>T |
Passed |
48419 |
2.43 % |
| Transversion |
T>A |
Passed |
48251 |
2.42 % |
| Transversion |
C>G |
Passed |
90273 |
4.53 % |
| Transversion |
G>C |
Passed |
90964 |
4.56 % |
| |
|
|
|
|
| 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 |
4.44 |
13144189 |
2957872 |
| Passed |
2.49 |
1421612 |
571876 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |