/EXTERNAL BLUEPRINT/variants/K006347_9_lane_gembs
BACK
SAMPLE K006347_9_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1138756469 |
717194696 |
62.98 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1138756469 |
100% |
1126926494 |
98.96 % |
11829975 |
1.04 % |
| |
|
|
|
|
|
|
| Passed |
719396614 |
63.17 % |
715605250 |
63.50 % |
3791364 |
0.53 % |
| Filtered |
419359855 |
36.83 % |
411321244 |
36.50 % |
8038611 |
1.12 % |
| |
|
|
|
|
|
|
| q20 |
369415419 |
88.09 % |
367906471 |
89.45 % |
1508948 |
18.77 % |
| q20,qd2 |
26359568 |
6.29 % |
20389924 |
4.96 % |
5969644 |
74.26 % |
| q20,mq40 |
13567644 |
3.24 % |
13462877 |
3.27 % |
104767 |
1.30 % |
| mq40 |
4957177 |
1.18 % |
4790142 |
1.16 % |
167035 |
2.08 % |
| q20,qd2,mq40 |
3079471 |
0.73 % |
2895294 |
0.70 % |
184177 |
2.29 % |
| qd2 |
1916320 |
0.46 % |
1824675 |
0.44 % |
91645 |
1.14 % |
| qd2,mq40 |
61026 |
0.01 % |
51861 |
0.01 % |
9165 |
0.11 % |
| q20,qd2,fs60 |
952 |
0.00 % |
0 |
0.00 % |
952 |
0.01 % |
| qd2,fs60,mq40 |
689 |
0.00 % |
0 |
0.00 % |
689 |
0.01 % |
| fs60 |
569 |
0.00 % |
0 |
0.00 % |
569 |
0.01 % |
| qd2,fs60 |
357 |
0.00 % |
0 |
0.00 % |
357 |
0.00 % |
| q20,qd2,fs60,mq40 |
340 |
0.00 % |
0 |
0.00 % |
340 |
0.00 % |
| fs60,mq40 |
319 |
0.00 % |
0 |
0.00 % |
319 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3962927 |
29.03 % |
| Transition |
G>A |
All |
1440515 |
10.55 % |
| Transition |
T>C |
All |
3871231 |
28.36 % |
| Transition |
C>T |
All |
1401820 |
10.27 % |
| Transversion |
A>C |
All |
235332 |
1.72 % |
| Transversion |
C>A |
All |
582645 |
4.27 % |
| Transversion |
T>G |
All |
242029 |
1.77 % |
| Transversion |
G>T |
All |
580684 |
4.25 % |
| Transversion |
A>T |
All |
474340 |
3.48 % |
| Transversion |
T>A |
All |
463968 |
3.40 % |
| Transversion |
C>G |
All |
199401 |
1.46 % |
| Transversion |
G>C |
All |
194453 |
1.42 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
428988 |
18.41 % |
| Transition |
G>A |
Passed |
386352 |
16.58 % |
| Transition |
T>C |
Passed |
428054 |
18.37 % |
| Transition |
C>T |
Passed |
386951 |
16.61 % |
| Transversion |
A>C |
Passed |
93614 |
4.02 % |
| Transversion |
C>A |
Passed |
87072 |
3.74 % |
| Transversion |
T>G |
Passed |
93555 |
4.02 % |
| Transversion |
G>T |
Passed |
87653 |
3.76 % |
| Transversion |
A>T |
Passed |
63502 |
2.73 % |
| Transversion |
T>A |
Passed |
63649 |
2.73 % |
| Transversion |
C>G |
Passed |
104781 |
4.50 % |
| Transversion |
G>C |
Passed |
105949 |
4.55 % |
| |
|
|
|
|
| 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 |
3.59 |
10676493 |
2972852 |
| Passed |
2.33 |
1630345 |
699775 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |