/EXTERNAL BLUEPRINT/variants/K006419_14_lane_gembs
BACK
SAMPLE K006419_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156864067 |
1044804375 |
90.31 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156864067 |
100% |
1144947702 |
98.97 % |
11916365 |
1.03 % |
| |
|
|
|
|
|
|
| Passed |
1045707508 |
90.39 % |
1042409278 |
91.04 % |
3298230 |
0.32 % |
| Filtered |
111156559 |
9.61 % |
102538424 |
8.96 % |
8618135 |
0.82 % |
| |
|
|
|
|
|
|
| q20 |
78408983 |
70.54 % |
77690934 |
75.77 % |
718049 |
8.33 % |
| q20,mq40 |
12661677 |
11.39 % |
12558982 |
12.25 % |
102695 |
1.19 % |
| q20,qd2 |
11489082 |
10.34 % |
4198909 |
4.09 % |
7290173 |
84.59 % |
| mq40 |
3726768 |
3.35 % |
3539072 |
3.45 % |
187696 |
2.18 % |
| q20,qd2,mq40 |
2997462 |
2.70 % |
2826365 |
2.76 % |
171097 |
1.99 % |
| qd2 |
1826704 |
1.64 % |
1687899 |
1.65 % |
138805 |
1.61 % |
| qd2,mq40 |
44390 |
0.04 % |
36263 |
0.04 % |
8127 |
0.09 % |
| qd2,fs60,mq40 |
680 |
0.00 % |
0 |
0.00 % |
680 |
0.01 % |
| fs60,mq40 |
375 |
0.00 % |
0 |
0.00 % |
375 |
0.00 % |
| qd2,fs60 |
203 |
0.00 % |
0 |
0.00 % |
203 |
0.00 % |
| fs60 |
124 |
0.00 % |
0 |
0.00 % |
124 |
0.00 % |
| q20,qd2,fs60,mq40 |
86 |
0.00 % |
0 |
0.00 % |
86 |
0.00 % |
| q20,qd2,fs60 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
4488934 |
33.03 % |
| Transition |
G>A |
All |
921026 |
6.78 % |
| Transition |
T>C |
All |
4427271 |
32.58 % |
| Transition |
C>T |
All |
929631 |
6.84 % |
| Transversion |
A>C |
All |
222036 |
1.63 % |
| Transversion |
C>A |
All |
538073 |
3.96 % |
| Transversion |
T>G |
All |
222971 |
1.64 % |
| Transversion |
G>T |
All |
527245 |
3.88 % |
| Transversion |
A>T |
All |
452782 |
3.33 % |
| Transversion |
T>A |
All |
450009 |
3.31 % |
| Transversion |
C>G |
All |
204421 |
1.50 % |
| Transversion |
G>C |
All |
204453 |
1.50 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
623239 |
17.36 % |
| Transition |
G>A |
Passed |
576221 |
16.05 % |
| Transition |
T>C |
Passed |
625183 |
17.41 % |
| Transition |
C>T |
Passed |
580958 |
16.18 % |
| Transversion |
A>C |
Passed |
151549 |
4.22 % |
| Transversion |
C>A |
Passed |
156705 |
4.36 % |
| Transversion |
T>G |
Passed |
152105 |
4.24 % |
| Transversion |
G>T |
Passed |
156513 |
4.36 % |
| Transversion |
A>T |
Passed |
133556 |
3.72 % |
| Transversion |
T>A |
Passed |
133989 |
3.73 % |
| Transversion |
C>G |
Passed |
150256 |
4.18 % |
| Transversion |
G>C |
Passed |
150164 |
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 |
3.82 |
10766862 |
2821990 |
| Passed |
2.03 |
2405601 |
1184837 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |