/EXTERNAL BLUEPRINT/variants/K006290_14_lane_gembs
BACK
SAMPLE K006290_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1007106720 |
421777699 |
41.88 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1007106720 |
100% |
991694183 |
98.47 % |
15412537 |
1.53 % |
| |
|
|
|
|
|
|
| Passed |
423185496 |
42.02 % |
420969882 |
42.45 % |
2215614 |
0.52 % |
| Filtered |
583921224 |
57.98 % |
570724301 |
57.55 % |
13196923 |
3.12 % |
| |
|
|
|
|
|
|
| q20 |
464658179 |
79.58 % |
462858068 |
81.10 % |
1800111 |
13.64 % |
| q20,qd2 |
75799636 |
12.98 % |
64883344 |
11.37 % |
10916292 |
82.72 % |
| qd2 |
16546863 |
2.83 % |
16460209 |
2.88 % |
86654 |
0.66 % |
| q20,mq40 |
16420690 |
2.81 % |
16334651 |
2.86 % |
86039 |
0.65 % |
| mq40 |
6442230 |
1.10 % |
6305149 |
1.10 % |
137081 |
1.04 % |
| q20,qd2,mq40 |
3942169 |
0.68 % |
3799685 |
0.67 % |
142484 |
1.08 % |
| qd2,mq40 |
95838 |
0.02 % |
83195 |
0.01 % |
12643 |
0.10 % |
| q20,qd2,fs60 |
4673 |
0.00 % |
0 |
0.00 % |
4673 |
0.04 % |
| qd2,fs60 |
4657 |
0.00 % |
0 |
0.00 % |
4657 |
0.04 % |
| qd2,fs60,mq40 |
2354 |
0.00 % |
0 |
0.00 % |
2354 |
0.02 % |
| fs60 |
2203 |
0.00 % |
0 |
0.00 % |
2203 |
0.02 % |
| q20,qd2,fs60,mq40 |
1045 |
0.00 % |
0 |
0.00 % |
1045 |
0.01 % |
| fs60,mq40 |
685 |
0.00 % |
0 |
0.00 % |
685 |
0.01 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
2438228 |
8.42 % |
| Transition |
G>A |
All |
11035323 |
38.09 % |
| Transition |
T>C |
All |
2308173 |
7.97 % |
| Transition |
C>T |
All |
10882498 |
37.56 % |
| Transversion |
A>C |
All |
179397 |
0.62 % |
| Transversion |
C>A |
All |
458122 |
1.58 % |
| Transversion |
T>G |
All |
190789 |
0.66 % |
| Transversion |
G>T |
All |
448327 |
1.55 % |
| Transversion |
A>T |
All |
339433 |
1.17 % |
| Transversion |
T>A |
All |
338091 |
1.17 % |
| Transversion |
C>G |
All |
182009 |
0.63 % |
| Transversion |
G>C |
All |
170512 |
0.59 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
234850 |
19.69 % |
| Transition |
G>A |
Passed |
210631 |
17.66 % |
| Transition |
T>C |
Passed |
233563 |
19.58 % |
| Transition |
C>T |
Passed |
210395 |
17.64 % |
| Transversion |
A>C |
Passed |
40528 |
3.40 % |
| Transversion |
C>A |
Passed |
35201 |
2.95 % |
| Transversion |
T>G |
Passed |
40090 |
3.36 % |
| Transversion |
G>T |
Passed |
35271 |
2.96 % |
| Transversion |
A>T |
Passed |
20722 |
1.74 % |
| Transversion |
T>A |
Passed |
20552 |
1.72 % |
| Transversion |
C>G |
Passed |
55479 |
4.65 % |
| Transversion |
G>C |
Passed |
55723 |
4.67 % |
| |
|
|
|
|
| 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 |
11.56 |
26664222 |
2306680 |
| Passed |
2.93 |
889439 |
303566 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |