/EXTERNAL BLUEPRINT/variants/K006414_11_lane_gembs
BACK
SAMPLE K006414_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157305933 |
1043759602 |
90.19 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157305933 |
100% |
1144810895 |
98.92 % |
12495038 |
1.08 % |
| |
|
|
|
|
|
|
| Passed |
1044623312 |
90.26 % |
1041260904 |
90.95 % |
3362408 |
0.32 % |
| Filtered |
112682621 |
9.74 % |
103549991 |
9.05 % |
9132630 |
0.87 % |
| |
|
|
|
|
|
|
| q20 |
73690874 |
65.40 % |
72983502 |
70.48 % |
707372 |
7.75 % |
| q20,qd2 |
13863530 |
12.30 % |
6206664 |
5.99 % |
7656866 |
83.84 % |
| q20,mq40 |
13633928 |
12.10 % |
13504227 |
13.04 % |
129701 |
1.42 % |
| mq40 |
4500085 |
3.99 % |
4277414 |
4.13 % |
222671 |
2.44 % |
| qd2 |
3685076 |
3.27 % |
3537126 |
3.42 % |
147950 |
1.62 % |
| q20,qd2,mq40 |
3254749 |
2.89 % |
2996681 |
2.89 % |
258068 |
2.83 % |
| qd2,mq40 |
53035 |
0.05 % |
44377 |
0.04 % |
8658 |
0.09 % |
| qd2,fs60,mq40 |
654 |
0.00 % |
0 |
0.00 % |
654 |
0.01 % |
| fs60,mq40 |
328 |
0.00 % |
0 |
0.00 % |
328 |
0.00 % |
| qd2,fs60 |
154 |
0.00 % |
0 |
0.00 % |
154 |
0.00 % |
| fs60 |
114 |
0.00 % |
0 |
0.00 % |
114 |
0.00 % |
| q20,qd2,fs60,mq40 |
70 |
0.00 % |
0 |
0.00 % |
70 |
0.00 % |
| q20,qd2,fs60 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
4278624 |
30.20 % |
| Transition |
G>A |
All |
1057790 |
7.47 % |
| Transition |
T>C |
All |
4231581 |
29.87 % |
| Transition |
C>T |
All |
1067329 |
7.53 % |
| Transversion |
A>C |
All |
218618 |
1.54 % |
| Transversion |
C>A |
All |
895305 |
6.32 % |
| Transversion |
T>G |
All |
219467 |
1.55 % |
| Transversion |
G>T |
All |
893743 |
6.31 % |
| Transversion |
A>T |
All |
445516 |
3.15 % |
| Transversion |
T>A |
All |
435175 |
3.07 % |
| Transversion |
C>G |
All |
210738 |
1.49 % |
| Transversion |
G>C |
All |
211936 |
1.50 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
630902 |
17.09 % |
| Transition |
G>A |
Passed |
606863 |
16.44 % |
| Transition |
T>C |
Passed |
633020 |
17.15 % |
| Transition |
C>T |
Passed |
612662 |
16.60 % |
| Transversion |
A>C |
Passed |
151763 |
4.11 % |
| Transversion |
C>A |
Passed |
162321 |
4.40 % |
| Transversion |
T>G |
Passed |
151976 |
4.12 % |
| Transversion |
G>T |
Passed |
162601 |
4.41 % |
| Transversion |
A>T |
Passed |
137199 |
3.72 % |
| Transversion |
T>A |
Passed |
137308 |
3.72 % |
| Transversion |
C>G |
Passed |
151963 |
4.12 % |
| Transversion |
G>C |
Passed |
152464 |
4.13 % |
| |
|
|
|
|
| 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 |
3.01 |
10635324 |
3530498 |
| Passed |
2.06 |
2483447 |
1207595 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |