/EXTERNAL BLUEPRINT/variants/K006314_21_lane_gembs
BACK
SAMPLE K006314_21_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1047066188 |
490620390 |
46.86 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1047066188 |
100% |
1028905829 |
98.27 % |
18160359 |
1.73 % |
| |
|
|
|
|
|
|
| Passed |
492485466 |
47.03 % |
489644360 |
47.59 % |
2841106 |
0.58 % |
| Filtered |
554580722 |
52.97 % |
539261469 |
52.41 % |
15319253 |
3.11 % |
| |
|
|
|
|
|
|
| q20 |
449826569 |
81.11 % |
447963189 |
83.07 % |
1863380 |
12.16 % |
| q20,qd2 |
69078775 |
12.46 % |
56119846 |
10.41 % |
12958929 |
84.59 % |
| q20,mq40 |
15366892 |
2.77 % |
15283818 |
2.83 % |
83074 |
0.54 % |
| qd2 |
10093655 |
1.82 % |
9997695 |
1.85 % |
95960 |
0.63 % |
| mq40 |
6619766 |
1.19 % |
6471794 |
1.20 % |
147972 |
0.97 % |
| q20,qd2,mq40 |
3501833 |
0.63 % |
3355301 |
0.62 % |
146532 |
0.96 % |
| qd2,mq40 |
80954 |
0.01 % |
69826 |
0.01 % |
11128 |
0.07 % |
| q20,qd2,fs60 |
3670 |
0.00 % |
0 |
0.00 % |
3670 |
0.02 % |
| qd2,fs60 |
3468 |
0.00 % |
0 |
0.00 % |
3468 |
0.02 % |
| fs60 |
2124 |
0.00 % |
0 |
0.00 % |
2124 |
0.01 % |
| qd2,fs60,mq40 |
1708 |
0.00 % |
0 |
0.00 % |
1708 |
0.01 % |
| q20,qd2,fs60,mq40 |
803 |
0.00 % |
0 |
0.00 % |
803 |
0.01 % |
| fs60,mq40 |
499 |
0.00 % |
0 |
0.00 % |
499 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
3256572 |
10.61 % |
| Transition |
G>A |
All |
11109845 |
36.21 % |
| Transition |
T>C |
All |
2897811 |
9.44 % |
| Transition |
C>T |
All |
10912122 |
35.56 % |
| Transversion |
A>C |
All |
206245 |
0.67 % |
| Transversion |
C>A |
All |
498222 |
1.62 % |
| Transversion |
T>G |
All |
236745 |
0.77 % |
| Transversion |
G>T |
All |
475229 |
1.55 % |
| Transversion |
A>T |
All |
354898 |
1.16 % |
| Transversion |
T>A |
All |
371992 |
1.21 % |
| Transversion |
C>G |
All |
189615 |
0.62 % |
| Transversion |
G>C |
All |
173115 |
0.56 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
288085 |
19.99 % |
| Transition |
G>A |
Passed |
247684 |
17.19 % |
| Transition |
T>C |
Passed |
286532 |
19.88 % |
| Transition |
C>T |
Passed |
246544 |
17.11 % |
| Transversion |
A>C |
Passed |
49441 |
3.43 % |
| Transversion |
C>A |
Passed |
43715 |
3.03 % |
| Transversion |
T>G |
Passed |
49179 |
3.41 % |
| Transversion |
G>T |
Passed |
44027 |
3.05 % |
| Transversion |
A>T |
Passed |
27681 |
1.92 % |
| Transversion |
T>A |
Passed |
27284 |
1.89 % |
| Transversion |
C>G |
Passed |
65280 |
4.53 % |
| Transversion |
G>C |
Passed |
65694 |
4.56 % |
| |
|
|
|
|
| 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 |
11.24 |
28176350 |
2506061 |
| Passed |
2.87 |
1068845 |
372301 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |