/EXTERNAL KNIH/variants/K006245_1_lane_gembs
BACK
SAMPLE K006245_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1176514366 |
489775903 |
41.63 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1176514366 |
100% |
1116821830 |
94.93 % |
59692536 |
5.07 % |
| |
|
|
|
|
|
|
| Passed |
504983966 |
42.92 % |
481824951 |
43.14 % |
23159015 |
4.59 % |
| Filtered |
671530400 |
57.08 % |
634996879 |
56.86 % |
36533521 |
7.23 % |
| |
|
|
|
|
|
|
| q20 |
604443550 |
90.01 % |
589819448 |
92.89 % |
14624102 |
40.03 % |
| q20,qd2 |
56410157 |
8.40 % |
35419176 |
5.58 % |
20990981 |
57.46 % |
| q20,mq40 |
4961438 |
0.74 % |
4860090 |
0.77 % |
101348 |
0.28 % |
| qd2 |
2986686 |
0.44 % |
2362672 |
0.37 % |
624014 |
1.71 % |
| q20,qd2,mq40 |
2299304 |
0.34 % |
2236599 |
0.35 % |
62705 |
0.17 % |
| mq40 |
415919 |
0.06 % |
289548 |
0.05 % |
126371 |
0.35 % |
| qd2,mq40 |
12605 |
0.00 % |
9346 |
0.00 % |
3259 |
0.01 % |
| q20,qd2,fs60 |
355 |
0.00 % |
0 |
0.00 % |
355 |
0.00 % |
| fs60 |
201 |
0.00 % |
0 |
0.00 % |
201 |
0.00 % |
| qd2,fs60 |
88 |
0.00 % |
0 |
0.00 % |
88 |
0.00 % |
| fs60,mq40 |
50 |
0.00 % |
0 |
0.00 % |
50 |
0.00 % |
| qd2,fs60,mq40 |
37 |
0.00 % |
0 |
0.00 % |
37 |
0.00 % |
| q20,qd2,fs60,mq40 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,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 |
19481799 |
31.38 % |
| Transition |
G>A |
All |
4970156 |
8.00 % |
| Transition |
T>C |
All |
19998782 |
32.21 % |
| Transition |
C>T |
All |
2985088 |
4.81 % |
| Transversion |
A>C |
All |
1341060 |
2.16 % |
| Transversion |
C>A |
All |
2675773 |
4.31 % |
| Transversion |
T>G |
All |
1643135 |
2.65 % |
| Transversion |
G>T |
All |
2397760 |
3.86 % |
| Transversion |
A>T |
All |
1870849 |
3.01 % |
| Transversion |
T>A |
All |
2307220 |
3.72 % |
| Transversion |
C>G |
All |
1212699 |
1.95 % |
| Transversion |
G>C |
All |
1208941 |
1.95 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2094731 |
24.95 % |
| Transition |
G>A |
Passed |
879951 |
10.48 % |
| Transition |
T>C |
Passed |
3084408 |
36.73 % |
| Transition |
C>T |
Passed |
539109 |
6.42 % |
| Transversion |
A>C |
Passed |
202181 |
2.41 % |
| Transversion |
C>A |
Passed |
286269 |
3.41 % |
| Transversion |
T>G |
Passed |
245205 |
2.92 % |
| Transversion |
G>T |
Passed |
221527 |
2.64 % |
| Transversion |
A>T |
Passed |
146283 |
1.74 % |
| Transversion |
T>A |
Passed |
231145 |
2.75 % |
| Transversion |
C>G |
Passed |
227183 |
2.71 % |
| Transversion |
G>C |
Passed |
238501 |
2.84 % |
| |
|
|
|
|
| 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 |
3.24 |
47435825 |
14657437 |
| Passed |
3.67 |
6598199 |
1798294 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |