/EXTERNAL BLUEPRINT/variants/K011938_K011939_2_lane_gembs
BACK
SAMPLE K011938_K011939_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
342836986 |
20072 |
0.01 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
342836986 |
100% |
341512157 |
99.61 % |
1324829 |
0.39 % |
| |
|
|
|
|
|
|
| Passed |
673303 |
0.20 % |
10152 |
0.00 % |
663151 |
98.49 % |
| Filtered |
342163683 |
99.80 % |
341502005 |
100.00 % |
661678 |
98.27 % |
| |
|
|
|
|
|
|
| q20 |
203336304 |
59.43 % |
202818651 |
59.39 % |
517653 |
78.23 % |
| q20,qd2 |
106819050 |
31.22 % |
106763082 |
31.26 % |
55968 |
8.46 % |
| q20,mq40 |
19373514 |
5.66 % |
19334515 |
5.66 % |
38999 |
5.89 % |
| q20,qd2,mq40 |
12586113 |
3.68 % |
12580488 |
3.68 % |
5625 |
0.85 % |
| mq40 |
46654 |
0.01 % |
3286 |
0.00 % |
43368 |
6.55 % |
| qd2 |
1942 |
0.00 % |
1911 |
0.00 % |
31 |
0.00 % |
| qd2,mq40 |
98 |
0.00 % |
72 |
0.00 % |
26 |
0.00 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
952228 |
21.86 % |
| Transition |
G>A |
All |
351650 |
8.07 % |
| Transition |
T>C |
All |
1277188 |
29.31 % |
| Transition |
C>T |
All |
175454 |
4.03 % |
| Transversion |
A>C |
All |
140078 |
3.22 % |
| Transversion |
C>A |
All |
268326 |
6.16 % |
| Transversion |
T>G |
All |
179849 |
4.13 % |
| Transversion |
G>T |
All |
245046 |
5.62 % |
| Transversion |
A>T |
All |
200115 |
4.59 % |
| Transversion |
T>A |
All |
279911 |
6.42 % |
| Transversion |
C>G |
All |
131855 |
3.03 % |
| Transversion |
G>C |
All |
155233 |
3.56 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1654 |
16.91 % |
| Transition |
G>A |
Passed |
1079 |
11.03 % |
| Transition |
T>C |
Passed |
2565 |
26.22 % |
| Transition |
C>T |
Passed |
641 |
6.55 % |
| Transversion |
A>C |
Passed |
362 |
3.70 % |
| Transversion |
C>A |
Passed |
621 |
6.35 % |
| Transversion |
T>G |
Passed |
495 |
5.06 % |
| Transversion |
G>T |
Passed |
476 |
4.87 % |
| Transversion |
A>T |
Passed |
266 |
2.72 % |
| Transversion |
T>A |
Passed |
525 |
5.37 % |
| Transversion |
C>G |
Passed |
479 |
4.90 % |
| Transversion |
G>C |
Passed |
621 |
6.35 % |
| |
|
|
|
|
| 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 |
1.72 |
2756520 |
1600413 |
| Passed |
1.54 |
5939 |
3845 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |