/EXTERNAL KNIH/variants/K006224_1_lane_gembs
BACK
SAMPLE K006224_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1151757547 |
1076117079 |
93.43 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1151757547 |
100% |
1141869663 |
99.14 % |
9887884 |
0.86 % |
| |
|
|
|
|
|
|
| Passed |
1076756087 |
93.49 % |
1073602501 |
94.02 % |
3153586 |
0.29 % |
| Filtered |
75001460 |
6.51 % |
68267162 |
5.98 % |
6734298 |
0.63 % |
| |
|
|
|
|
|
|
| q20 |
41387160 |
55.18 % |
40867759 |
59.86 % |
519401 |
7.71 % |
| q20,mq40 |
13087282 |
17.45 % |
12949488 |
18.97 % |
137794 |
2.05 % |
| q20,qd2 |
7479433 |
9.97 % |
2359079 |
3.46 % |
5120354 |
76.03 % |
| mq40 |
7316059 |
9.75 % |
7007566 |
10.26 % |
308493 |
4.58 % |
| q20,qd2,mq40 |
3006133 |
4.01 % |
2752212 |
4.03 % |
253921 |
3.77 % |
| qd2 |
2632811 |
3.51 % |
2258993 |
3.31 % |
373818 |
5.55 % |
| qd2,mq40 |
87328 |
0.12 % |
72065 |
0.11 % |
15263 |
0.23 % |
| qd2,fs60,mq40 |
1917 |
0.00 % |
0 |
0.00 % |
1917 |
0.03 % |
| fs60 |
1010 |
0.00 % |
0 |
0.00 % |
1010 |
0.01 % |
| q20,qd2,fs60 |
823 |
0.00 % |
0 |
0.00 % |
823 |
0.01 % |
| fs60,mq40 |
722 |
0.00 % |
0 |
0.00 % |
722 |
0.01 % |
| qd2,fs60 |
600 |
0.00 % |
0 |
0.00 % |
600 |
0.01 % |
| q20,qd2,fs60,mq40 |
180 |
0.00 % |
0 |
0.00 % |
180 |
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 |
3825576 |
32.67 % |
| Transition |
G>A |
All |
922373 |
7.88 % |
| Transition |
T>C |
All |
3794566 |
32.40 % |
| Transition |
C>T |
All |
929243 |
7.93 % |
| Transversion |
A>C |
All |
211883 |
1.81 % |
| Transversion |
C>A |
All |
396665 |
3.39 % |
| Transversion |
T>G |
All |
213632 |
1.82 % |
| Transversion |
G>T |
All |
388395 |
3.32 % |
| Transversion |
A>T |
All |
311996 |
2.66 % |
| Transversion |
T>A |
All |
303173 |
2.59 % |
| Transversion |
C>G |
All |
206863 |
1.77 % |
| Transversion |
G>C |
All |
206845 |
1.77 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
702434 |
18.12 % |
| Transition |
G>A |
Passed |
624029 |
16.10 % |
| Transition |
T>C |
Passed |
705908 |
18.21 % |
| Transition |
C>T |
Passed |
630332 |
16.26 % |
| Transversion |
A>C |
Passed |
153164 |
3.95 % |
| Transversion |
C>A |
Passed |
160181 |
4.13 % |
| Transversion |
T>G |
Passed |
153374 |
3.96 % |
| Transversion |
G>T |
Passed |
159235 |
4.11 % |
| Transversion |
A>T |
Passed |
138749 |
3.58 % |
| Transversion |
T>A |
Passed |
138115 |
3.56 % |
| Transversion |
C>G |
Passed |
154782 |
3.99 % |
| Transversion |
G>C |
Passed |
155275 |
4.01 % |
| |
|
|
|
|
| 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 |
4.23 |
9471758 |
2239452 |
| Passed |
2.20 |
2662703 |
1212875 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |