/EXTERNAL BLUEPRINT/variants/K006426_14_lane_gembs
BACK
SAMPLE K006426_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1152394810 |
1048182266 |
90.96 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1152394810 |
100% |
1139722406 |
98.90 % |
12672404 |
1.10 % |
| |
|
|
|
|
|
|
| Passed |
1049104868 |
91.04 % |
1045609059 |
91.74 % |
3495809 |
0.33 % |
| Filtered |
103289942 |
8.96 % |
94113347 |
8.26 % |
9176595 |
0.87 % |
| |
|
|
|
|
|
|
| q20 |
69846926 |
67.62 % |
69097517 |
73.42 % |
749409 |
8.17 % |
| q20,mq40 |
12434360 |
12.04 % |
12329880 |
13.10 % |
104480 |
1.14 % |
| q20,qd2 |
12174827 |
11.79 % |
4359631 |
4.63 % |
7815196 |
85.16 % |
| mq40 |
3635204 |
3.52 % |
3439876 |
3.66 % |
195328 |
2.13 % |
| q20,qd2,mq40 |
3077238 |
2.98 % |
2909700 |
3.09 % |
167538 |
1.83 % |
| qd2 |
2078438 |
2.01 % |
1943188 |
2.06 % |
135250 |
1.47 % |
| qd2,mq40 |
41825 |
0.04 % |
33555 |
0.04 % |
8270 |
0.09 % |
| qd2,fs60,mq40 |
522 |
0.00 % |
0 |
0.00 % |
522 |
0.01 % |
| fs60,mq40 |
276 |
0.00 % |
0 |
0.00 % |
276 |
0.00 % |
| qd2,fs60 |
155 |
0.00 % |
0 |
0.00 % |
155 |
0.00 % |
| fs60 |
85 |
0.00 % |
0 |
0.00 % |
85 |
0.00 % |
| q20,qd2,fs60,mq40 |
60 |
0.00 % |
0 |
0.00 % |
60 |
0.00 % |
| q20,qd2,fs60 |
25 |
0.00 % |
0 |
0.00 % |
25 |
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 |
4746012 |
33.20 % |
| Transition |
G>A |
All |
999018 |
6.99 % |
| Transition |
T>C |
All |
4716895 |
33.00 % |
| Transition |
C>T |
All |
1008278 |
7.05 % |
| Transversion |
A>C |
All |
222958 |
1.56 % |
| Transversion |
C>A |
All |
532420 |
3.72 % |
| Transversion |
T>G |
All |
225504 |
1.58 % |
| Transversion |
G>T |
All |
524303 |
3.67 % |
| Transversion |
A>T |
All |
455537 |
3.19 % |
| Transversion |
T>A |
All |
451950 |
3.16 % |
| Transversion |
C>G |
All |
206130 |
1.44 % |
| Transversion |
G>C |
All |
205646 |
1.44 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
645786 |
17.31 % |
| Transition |
G>A |
Passed |
606246 |
16.25 % |
| Transition |
T>C |
Passed |
648455 |
17.38 % |
| Transition |
C>T |
Passed |
609139 |
16.32 % |
| Transversion |
A>C |
Passed |
155652 |
4.17 % |
| Transversion |
C>A |
Passed |
162400 |
4.35 % |
| Transversion |
T>G |
Passed |
157012 |
4.21 % |
| Transversion |
G>T |
Passed |
161974 |
4.34 % |
| Transversion |
A>T |
Passed |
137653 |
3.69 % |
| Transversion |
T>A |
Passed |
138110 |
3.70 % |
| Transversion |
C>G |
Passed |
154469 |
4.14 % |
| Transversion |
G>C |
Passed |
154740 |
4.15 % |
| |
|
|
|
|
| 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 |
4.06 |
11470203 |
2824448 |
| Passed |
2.05 |
2509626 |
1222010 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |