/EXTERNAL KNIH/variants/K006223_1_lane_gembs
BACK
SAMPLE K006223_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157268814 |
1028774871 |
88.90 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157268814 |
100% |
1141487551 |
98.64 % |
15781263 |
1.36 % |
| |
|
|
|
|
|
|
| Passed |
1030706808 |
89.06 % |
1026294298 |
89.91 % |
4412510 |
0.43 % |
| Filtered |
126562006 |
10.94 % |
115193253 |
10.09 % |
11368753 |
1.10 % |
| |
|
|
|
|
|
|
| q20 |
86686180 |
68.49 % |
85380360 |
74.12 % |
1305820 |
11.49 % |
| q20,mq40 |
14119398 |
11.16 % |
13961768 |
12.12 % |
157630 |
1.39 % |
| q20,qd2 |
11844498 |
9.36 % |
2943690 |
2.56 % |
8900808 |
78.29 % |
| mq40 |
8233656 |
6.51 % |
7913655 |
6.87 % |
320001 |
2.81 % |
| q20,qd2,mq40 |
3024581 |
2.39 % |
2755578 |
2.39 % |
269003 |
2.37 % |
| qd2 |
2557529 |
2.02 % |
2162529 |
1.88 % |
395000 |
3.47 % |
| qd2,mq40 |
90821 |
0.07 % |
75673 |
0.07 % |
15148 |
0.13 % |
| qd2,fs60,mq40 |
1538 |
0.00 % |
0 |
0.00 % |
1538 |
0.01 % |
| fs60 |
1106 |
0.00 % |
0 |
0.00 % |
1106 |
0.01 % |
| q20,qd2,fs60 |
914 |
0.00 % |
0 |
0.00 % |
914 |
0.01 % |
| qd2,fs60 |
857 |
0.00 % |
0 |
0.00 % |
857 |
0.01 % |
| fs60,mq40 |
697 |
0.00 % |
0 |
0.00 % |
697 |
0.01 % |
| q20,qd2,fs60,mq40 |
228 |
0.00 % |
0 |
0.00 % |
228 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
6684521 |
37.88 % |
| Transition |
G>A |
All |
1041006 |
5.90 % |
| Transition |
T>C |
All |
6654694 |
37.71 % |
| Transition |
C>T |
All |
1034847 |
5.86 % |
| Transversion |
A>C |
All |
232581 |
1.32 % |
| Transversion |
C>A |
All |
361257 |
2.05 % |
| Transversion |
T>G |
All |
235628 |
1.34 % |
| Transversion |
G>T |
All |
359199 |
2.04 % |
| Transversion |
A>T |
All |
313457 |
1.78 % |
| Transversion |
T>A |
All |
306086 |
1.73 % |
| Transversion |
C>G |
All |
212108 |
1.20 % |
| Transversion |
G>C |
All |
211462 |
1.20 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
734568 |
19.64 % |
| Transition |
G>A |
Passed |
568766 |
15.21 % |
| Transition |
T>C |
Passed |
738818 |
19.75 % |
| Transition |
C>T |
Passed |
571244 |
15.27 % |
| Transversion |
A>C |
Passed |
145958 |
3.90 % |
| Transversion |
C>A |
Passed |
144853 |
3.87 % |
| Transversion |
T>G |
Passed |
146601 |
3.92 % |
| Transversion |
G>T |
Passed |
144529 |
3.86 % |
| Transversion |
A>T |
Passed |
124973 |
3.34 % |
| Transversion |
T>A |
Passed |
124812 |
3.34 % |
| Transversion |
C>G |
Passed |
147551 |
3.94 % |
| Transversion |
G>C |
Passed |
147786 |
3.95 % |
| |
|
|
|
|
| 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 |
6.91 |
15415068 |
2231778 |
| Passed |
2.32 |
2613396 |
1127063 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |