/EXTERNAL BLUEPRINT/variants/K006325_15_lane_gembs
BACK
SAMPLE K006325_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1082932299 |
570483130 |
52.68 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1082932299 |
100% |
1063105416 |
98.17 % |
19826883 |
1.83 % |
| |
|
|
|
|
|
|
| Passed |
572114252 |
52.83 % |
569299983 |
53.55 % |
2814269 |
0.49 % |
| Filtered |
510818047 |
47.17 % |
493805433 |
46.45 % |
17012614 |
2.97 % |
| |
|
|
|
|
|
|
| q20 |
413604611 |
80.97 % |
411792053 |
83.39 % |
1812558 |
10.65 % |
| q20,qd2 |
63236335 |
12.38 % |
48648472 |
9.85 % |
14587863 |
85.75 % |
| q20,mq40 |
15413408 |
3.02 % |
15304598 |
3.10 % |
108810 |
0.64 % |
| mq40 |
7842045 |
1.54 % |
7677131 |
1.55 % |
164914 |
0.97 % |
| qd2 |
7108223 |
1.39 % |
7002332 |
1.42 % |
105891 |
0.62 % |
| q20,qd2,mq40 |
3502715 |
0.69 % |
3295950 |
0.67 % |
206765 |
1.22 % |
| qd2,mq40 |
97212 |
0.02 % |
84897 |
0.02 % |
12315 |
0.07 % |
| q20,qd2,fs60 |
4952 |
0.00 % |
0 |
0.00 % |
4952 |
0.03 % |
| fs60 |
2795 |
0.00 % |
0 |
0.00 % |
2795 |
0.02 % |
| qd2,fs60 |
2753 |
0.00 % |
0 |
0.00 % |
2753 |
0.02 % |
| qd2,fs60,mq40 |
1649 |
0.00 % |
0 |
0.00 % |
1649 |
0.01 % |
| q20,qd2,fs60,mq40 |
753 |
0.00 % |
0 |
0.00 % |
753 |
0.00 % |
| fs60,mq40 |
588 |
0.00 % |
0 |
0.00 % |
588 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
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 |
3131799 |
9.76 % |
| Transition |
G>A |
All |
11777801 |
36.72 % |
| Transition |
T>C |
All |
2889982 |
9.01 % |
| Transition |
C>T |
All |
11590682 |
36.13 % |
| Transversion |
A>C |
All |
205910 |
0.64 % |
| Transversion |
C>A |
All |
531647 |
1.66 % |
| Transversion |
T>G |
All |
226570 |
0.71 % |
| Transversion |
G>T |
All |
520980 |
1.62 % |
| Transversion |
A>T |
All |
413373 |
1.29 % |
| Transversion |
T>A |
All |
415614 |
1.30 % |
| Transversion |
C>G |
All |
191351 |
0.60 % |
| Transversion |
G>C |
All |
180562 |
0.56 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
331840 |
19.32 % |
| Transition |
G>A |
Passed |
297815 |
17.34 % |
| Transition |
T>C |
Passed |
331384 |
19.29 % |
| Transition |
C>T |
Passed |
296984 |
17.29 % |
| Transversion |
A>C |
Passed |
61343 |
3.57 % |
| Transversion |
C>A |
Passed |
55026 |
3.20 % |
| Transversion |
T>G |
Passed |
61028 |
3.55 % |
| Transversion |
G>T |
Passed |
55409 |
3.23 % |
| Transversion |
A>T |
Passed |
36045 |
2.10 % |
| Transversion |
T>A |
Passed |
36028 |
2.10 % |
| Transversion |
C>G |
Passed |
77460 |
4.51 % |
| Transversion |
G>C |
Passed |
77565 |
4.52 % |
| |
|
|
|
|
| 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 |
10.94 |
29390264 |
2686007 |
| Passed |
2.74 |
1258023 |
459904 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |