/EXTERNAL BLUEPRINT/variants/K006417_12_lane_gembs
BACK
SAMPLE K006417_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156597232 |
1044201290 |
90.28 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156597232 |
100% |
1144908586 |
98.99 % |
11688646 |
1.01 % |
| |
|
|
|
|
|
|
| Passed |
1045034288 |
90.35 % |
1041828894 |
91.00 % |
3205394 |
0.31 % |
| Filtered |
111562944 |
9.65 % |
103079692 |
9.00 % |
8483252 |
0.81 % |
| |
|
|
|
|
|
|
| q20 |
76997574 |
69.02 % |
76312438 |
74.03 % |
685136 |
8.08 % |
| q20,mq40 |
13008507 |
11.66 % |
12895599 |
12.51 % |
112908 |
1.33 % |
| q20,qd2 |
12067030 |
10.82 % |
4935263 |
4.79 % |
7131767 |
84.07 % |
| mq40 |
3878037 |
3.48 % |
3678037 |
3.57 % |
200000 |
2.36 % |
| q20,qd2,mq40 |
3195834 |
2.86 % |
2987736 |
2.90 % |
208098 |
2.45 % |
| qd2 |
2367143 |
2.12 % |
2230999 |
2.16 % |
136144 |
1.60 % |
| qd2,mq40 |
47586 |
0.04 % |
39620 |
0.04 % |
7966 |
0.09 % |
| qd2,fs60,mq40 |
573 |
0.00 % |
0 |
0.00 % |
573 |
0.01 % |
| fs60,mq40 |
325 |
0.00 % |
0 |
0.00 % |
325 |
0.00 % |
| qd2,fs60 |
142 |
0.00 % |
0 |
0.00 % |
142 |
0.00 % |
| fs60 |
90 |
0.00 % |
0 |
0.00 % |
90 |
0.00 % |
| q20,qd2,fs60,mq40 |
66 |
0.00 % |
0 |
0.00 % |
66 |
0.00 % |
| q20,qd2,fs60 |
32 |
0.00 % |
0 |
0.00 % |
32 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
4200959 |
31.16 % |
| Transition |
G>A |
All |
952690 |
7.07 % |
| Transition |
T>C |
All |
4167642 |
30.91 % |
| Transition |
C>T |
All |
957755 |
7.10 % |
| Transversion |
A>C |
All |
217934 |
1.62 % |
| Transversion |
C>A |
All |
712348 |
5.28 % |
| Transversion |
T>G |
All |
219151 |
1.63 % |
| Transversion |
G>T |
All |
704042 |
5.22 % |
| Transversion |
A>T |
All |
467214 |
3.47 % |
| Transversion |
T>A |
All |
466575 |
3.46 % |
| Transversion |
C>G |
All |
206801 |
1.53 % |
| Transversion |
G>C |
All |
207951 |
1.54 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
631666 |
17.25 % |
| Transition |
G>A |
Passed |
594124 |
16.23 % |
| Transition |
T>C |
Passed |
633339 |
17.30 % |
| Transition |
C>T |
Passed |
598131 |
16.33 % |
| Transversion |
A>C |
Passed |
152797 |
4.17 % |
| Transversion |
C>A |
Passed |
159618 |
4.36 % |
| Transversion |
T>G |
Passed |
153570 |
4.19 % |
| Transversion |
G>T |
Passed |
159486 |
4.36 % |
| Transversion |
A>T |
Passed |
136398 |
3.73 % |
| Transversion |
T>A |
Passed |
136666 |
3.73 % |
| Transversion |
C>G |
Passed |
152718 |
4.17 % |
| Transversion |
G>C |
Passed |
153167 |
4.18 % |
| |
|
|
|
|
| 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 |
3.21 |
10279046 |
3202016 |
| Passed |
2.04 |
2457260 |
1204420 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |