/EXTERNAL KNIH/variants/K006228_1_lane_gembs
BACK
SAMPLE K006228_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157122811 |
1037169037 |
89.63 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157122811 |
100% |
1141091398 |
98.61 % |
16031413 |
1.39 % |
| |
|
|
|
|
|
|
| Passed |
1038853468 |
89.78 % |
1034594655 |
90.67 % |
4258813 |
0.41 % |
| Filtered |
118269343 |
10.22 % |
106496743 |
9.33 % |
11772600 |
1.13 % |
| |
|
|
|
|
|
|
| q20 |
77784547 |
65.77 % |
76608976 |
71.94 % |
1175571 |
9.99 % |
| q20,mq40 |
14885836 |
12.59 % |
14732672 |
13.83 % |
153164 |
1.30 % |
| q20,qd2 |
11907853 |
10.07 % |
2546778 |
2.39 % |
9361075 |
79.52 % |
| mq40 |
8404223 |
7.11 % |
8073728 |
7.58 % |
330495 |
2.81 % |
| q20,qd2,mq40 |
2986748 |
2.53 % |
2709436 |
2.54 % |
277312 |
2.36 % |
| qd2 |
2214824 |
1.87 % |
1757725 |
1.65 % |
457099 |
3.88 % |
| qd2,mq40 |
81529 |
0.07 % |
67428 |
0.06 % |
14101 |
0.12 % |
| qd2,fs60,mq40 |
1433 |
0.00 % |
0 |
0.00 % |
1433 |
0.01 % |
| fs60 |
722 |
0.00 % |
0 |
0.00 % |
722 |
0.01 % |
| fs60,mq40 |
584 |
0.00 % |
0 |
0.00 % |
584 |
0.00 % |
| qd2,fs60 |
549 |
0.00 % |
0 |
0.00 % |
549 |
0.00 % |
| q20,qd2,fs60 |
321 |
0.00 % |
0 |
0.00 % |
321 |
0.00 % |
| q20,qd2,fs60,mq40 |
170 |
0.00 % |
0 |
0.00 % |
170 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
6965130 |
38.99 % |
| Transition |
G>A |
All |
892215 |
4.99 % |
| Transition |
T>C |
All |
6907715 |
38.67 % |
| Transition |
C>T |
All |
893963 |
5.00 % |
| Transversion |
A>C |
All |
235391 |
1.32 % |
| Transversion |
C>A |
All |
349369 |
1.96 % |
| Transversion |
T>G |
All |
238088 |
1.33 % |
| Transversion |
G>T |
All |
346238 |
1.94 % |
| Transversion |
A>T |
All |
306976 |
1.72 % |
| Transversion |
T>A |
All |
299572 |
1.68 % |
| Transversion |
C>G |
All |
215325 |
1.21 % |
| Transversion |
G>C |
All |
213427 |
1.19 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
772040 |
20.00 % |
| Transition |
G>A |
Passed |
576532 |
14.94 % |
| Transition |
T>C |
Passed |
777225 |
20.14 % |
| Transition |
C>T |
Passed |
579238 |
15.01 % |
| Transversion |
A>C |
Passed |
149465 |
3.87 % |
| Transversion |
C>A |
Passed |
148281 |
3.84 % |
| Transversion |
T>G |
Passed |
150368 |
3.90 % |
| Transversion |
G>T |
Passed |
148472 |
3.85 % |
| Transversion |
A>T |
Passed |
129207 |
3.35 % |
| Transversion |
T>A |
Passed |
129106 |
3.34 % |
| Transversion |
C>G |
Passed |
150179 |
3.89 % |
| Transversion |
G>C |
Passed |
149684 |
3.88 % |
| |
|
|
|
|
| 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 |
7.10 |
15659023 |
2204386 |
| Passed |
2.34 |
2705035 |
1154762 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |