/EXTERNAL BLUEPRINT/variants/K006367_20_lane_gembs
BACK
SAMPLE K006367_20_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1139770057 |
637344249 |
55.92 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1139770057 |
100% |
1121074361 |
98.36 % |
18695696 |
1.64 % |
| |
|
|
|
|
|
|
| Passed |
640421031 |
56.19 % |
635782555 |
56.71 % |
4638476 |
0.72 % |
| Filtered |
499349026 |
43.81 % |
485291806 |
43.29 % |
14057220 |
2.19 % |
| |
|
|
|
|
|
|
| q20 |
429879869 |
86.09 % |
425517721 |
87.68 % |
4362148 |
31.03 % |
| q20,qd2 |
34762315 |
6.96 % |
25927293 |
5.34 % |
8835022 |
62.85 % |
| q20,mq40 |
16605538 |
3.33 % |
16394616 |
3.38 % |
210922 |
1.50 % |
| qd2 |
7604329 |
1.52 % |
7506494 |
1.55 % |
97835 |
0.70 % |
| mq40 |
6486601 |
1.30 % |
6280361 |
1.29 % |
206240 |
1.47 % |
| q20,qd2,mq40 |
3913316 |
0.78 % |
3582963 |
0.74 % |
330353 |
2.35 % |
| qd2,mq40 |
93537 |
0.02 % |
82358 |
0.02 % |
11179 |
0.08 % |
| qd2,fs60,mq40 |
1033 |
0.00 % |
0 |
0.00 % |
1033 |
0.01 % |
| q20,qd2,fs60 |
584 |
0.00 % |
0 |
0.00 % |
584 |
0.00 % |
| qd2,fs60 |
569 |
0.00 % |
0 |
0.00 % |
569 |
0.00 % |
| fs60 |
562 |
0.00 % |
0 |
0.00 % |
562 |
0.00 % |
| fs60,mq40 |
441 |
0.00 % |
0 |
0.00 % |
441 |
0.00 % |
| q20,qd2,fs60,mq40 |
331 |
0.00 % |
0 |
0.00 % |
331 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
5288607 |
25.20 % |
| Transition |
G>A |
All |
1785678 |
8.51 % |
| Transition |
T>C |
All |
4040876 |
19.25 % |
| Transition |
C>T |
All |
1777994 |
8.47 % |
| Transversion |
A>C |
All |
448030 |
2.13 % |
| Transversion |
C>A |
All |
1827873 |
8.71 % |
| Transversion |
T>G |
All |
544731 |
2.60 % |
| Transversion |
G>T |
All |
1793215 |
8.54 % |
| Transversion |
A>T |
All |
1367046 |
6.51 % |
| Transversion |
T>A |
All |
1400818 |
6.67 % |
| Transversion |
C>G |
All |
377761 |
1.80 % |
| Transversion |
G>C |
All |
334552 |
1.59 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
402291 |
18.58 % |
| Transition |
G>A |
Passed |
355978 |
16.44 % |
| Transition |
T>C |
Passed |
389871 |
18.01 % |
| Transition |
C>T |
Passed |
356244 |
16.46 % |
| Transversion |
A>C |
Passed |
84313 |
3.89 % |
| Transversion |
C>A |
Passed |
84978 |
3.93 % |
| Transversion |
T>G |
Passed |
85110 |
3.93 % |
| Transversion |
G>T |
Passed |
84944 |
3.92 % |
| Transversion |
A>T |
Passed |
61342 |
2.83 % |
| Transversion |
T>A |
Passed |
60659 |
2.80 % |
| Transversion |
C>G |
Passed |
99683 |
4.60 % |
| Transversion |
G>C |
Passed |
99324 |
4.59 % |
| |
|
|
|
|
| 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 |
1.59 |
12893155 |
8094026 |
| Passed |
2.28 |
1504384 |
660353 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |