/EXTERNAL BLUEPRINT/variants/K006424_14_lane_gembs
BACK
SAMPLE K006424_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1151928242 |
1046030678 |
90.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1151928242 |
100% |
1139356771 |
98.91 % |
12571471 |
1.09 % |
| |
|
|
|
|
|
|
| Passed |
1046964805 |
90.89 % |
1043462407 |
91.58 % |
3502398 |
0.33 % |
| Filtered |
104963437 |
9.11 % |
95894364 |
8.42 % |
9069073 |
0.87 % |
| |
|
|
|
|
|
|
| q20 |
71228018 |
67.86 % |
70482539 |
73.50 % |
745479 |
8.22 % |
| q20,mq40 |
12547437 |
11.95 % |
12443726 |
12.98 % |
103711 |
1.14 % |
| q20,qd2 |
11990811 |
11.42 % |
4279275 |
4.46 % |
7711536 |
85.03 % |
| mq40 |
3971946 |
3.78 % |
3780841 |
3.94 % |
191105 |
2.11 % |
| q20,qd2,mq40 |
3028513 |
2.89 % |
2853461 |
2.98 % |
175052 |
1.93 % |
| qd2 |
2155272 |
2.05 % |
2021817 |
2.11 % |
133455 |
1.47 % |
| qd2,mq40 |
40190 |
0.04 % |
32705 |
0.03 % |
7485 |
0.08 % |
| qd2,fs60,mq40 |
615 |
0.00 % |
0 |
0.00 % |
615 |
0.01 % |
| fs60,mq40 |
283 |
0.00 % |
0 |
0.00 % |
283 |
0.00 % |
| qd2,fs60 |
173 |
0.00 % |
0 |
0.00 % |
173 |
0.00 % |
| fs60 |
83 |
0.00 % |
0 |
0.00 % |
83 |
0.00 % |
| q20,qd2,fs60,mq40 |
64 |
0.00 % |
0 |
0.00 % |
64 |
0.00 % |
| q20,qd2,fs60 |
27 |
0.00 % |
0 |
0.00 % |
27 |
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 |
4723161 |
33.31 % |
| Transition |
G>A |
All |
989772 |
6.98 % |
| Transition |
T>C |
All |
4681555 |
33.02 % |
| Transition |
C>T |
All |
999299 |
7.05 % |
| Transversion |
A>C |
All |
221500 |
1.56 % |
| Transversion |
C>A |
All |
528696 |
3.73 % |
| Transversion |
T>G |
All |
222755 |
1.57 % |
| Transversion |
G>T |
All |
521054 |
3.67 % |
| Transversion |
A>T |
All |
443627 |
3.13 % |
| Transversion |
T>A |
All |
438571 |
3.09 % |
| Transversion |
C>G |
All |
204689 |
1.44 % |
| Transversion |
G>C |
All |
205054 |
1.45 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
638407 |
17.18 % |
| Transition |
G>A |
Passed |
606044 |
16.31 % |
| Transition |
T>C |
Passed |
641305 |
17.26 % |
| Transition |
C>T |
Passed |
609894 |
16.42 % |
| Transversion |
A>C |
Passed |
155847 |
4.19 % |
| Transversion |
C>A |
Passed |
162006 |
4.36 % |
| Transversion |
T>G |
Passed |
156140 |
4.20 % |
| Transversion |
G>T |
Passed |
161944 |
4.36 % |
| Transversion |
A>T |
Passed |
137400 |
3.70 % |
| Transversion |
T>A |
Passed |
137248 |
3.69 % |
| Transversion |
C>G |
Passed |
154207 |
4.15 % |
| Transversion |
G>C |
Passed |
154793 |
4.17 % |
| |
|
|
|
|
| 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 |
4.09 |
11393787 |
2785946 |
| Passed |
2.05 |
2495650 |
1219585 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |