/EXTERNAL BLUEPRINT/variants/K006369_13_lane_gembs
BACK
SAMPLE K006369_13_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1139886253 |
776291398 |
68.10 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1139886253 |
100% |
1121771195 |
98.41 % |
18115058 |
1.59 % |
| |
|
|
|
|
|
|
| Passed |
777945816 |
68.25 % |
774659214 |
69.06 % |
3286602 |
0.42 % |
| Filtered |
361940437 |
31.75 % |
347111981 |
30.94 % |
14828456 |
1.91 % |
| |
|
|
|
|
|
|
| q20 |
298688899 |
82.52 % |
297197551 |
85.62 % |
1491348 |
10.06 % |
| q20,qd2 |
36606288 |
10.11 % |
23918071 |
6.89 % |
12688217 |
85.57 % |
| q20,mq40 |
13350088 |
3.69 % |
13238802 |
3.81 % |
111286 |
0.75 % |
| mq40 |
7631263 |
2.11 % |
7450233 |
2.15 % |
181030 |
1.22 % |
| q20,qd2,mq40 |
2919316 |
0.81 % |
2703965 |
0.78 % |
215351 |
1.45 % |
| qd2 |
2631678 |
0.73 % |
2513113 |
0.72 % |
118565 |
0.80 % |
| qd2,mq40 |
103593 |
0.03 % |
90246 |
0.03 % |
13347 |
0.09 % |
| q20,qd2,fs60 |
3302 |
0.00 % |
0 |
0.00 % |
3302 |
0.02 % |
| fs60 |
2142 |
0.00 % |
0 |
0.00 % |
2142 |
0.01 % |
| qd2,fs60,mq40 |
1438 |
0.00 % |
0 |
0.00 % |
1438 |
0.01 % |
| qd2,fs60 |
1261 |
0.00 % |
0 |
0.00 % |
1261 |
0.01 % |
| fs60,mq40 |
602 |
0.00 % |
0 |
0.00 % |
602 |
0.00 % |
| q20,qd2,fs60,mq40 |
563 |
0.00 % |
0 |
0.00 % |
563 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3359243 |
14.76 % |
| Transition |
G>A |
All |
6757819 |
29.69 % |
| Transition |
T>C |
All |
3194508 |
14.03 % |
| Transition |
C>T |
All |
6635679 |
29.15 % |
| Transversion |
A>C |
All |
224723 |
0.99 % |
| Transversion |
C>A |
All |
579866 |
2.55 % |
| Transversion |
T>G |
All |
234374 |
1.03 % |
| Transversion |
G>T |
All |
577703 |
2.54 % |
| Transversion |
A>T |
All |
408756 |
1.80 % |
| Transversion |
T>A |
All |
401984 |
1.77 % |
| Transversion |
C>G |
All |
196157 |
0.86 % |
| Transversion |
G>C |
All |
190572 |
0.84 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
446346 |
18.20 % |
| Transition |
G>A |
Passed |
417364 |
17.02 % |
| Transition |
T>C |
Passed |
445667 |
18.18 % |
| Transition |
C>T |
Passed |
418805 |
17.08 % |
| Transversion |
A>C |
Passed |
96413 |
3.93 % |
| Transversion |
C>A |
Passed |
90569 |
3.69 % |
| Transversion |
T>G |
Passed |
96350 |
3.93 % |
| Transversion |
G>T |
Passed |
90442 |
3.69 % |
| Transversion |
A>T |
Passed |
66337 |
2.71 % |
| Transversion |
T>A |
Passed |
66380 |
2.71 % |
| Transversion |
C>G |
Passed |
108207 |
4.41 % |
| Transversion |
G>C |
Passed |
109055 |
4.45 % |
| |
|
|
|
|
| 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 |
7.09 |
19947249 |
2814135 |
| Passed |
2.39 |
1728182 |
723753 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |