/cemt/variants/K005743_0_lane_gembs
BACK
SAMPLE K005743_0_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1171334993 |
712733236 |
60.85 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1171334993 |
100% |
1151873766 |
98.34 % |
19461227 |
1.66 % |
| |
|
|
|
|
|
|
| Passed |
717153173 |
61.23 % |
710048589 |
61.64 % |
7104584 |
0.99 % |
| Filtered |
454181820 |
38.77 % |
441825177 |
38.36 % |
12356643 |
1.72 % |
| |
|
|
|
|
|
|
| q20 |
416111229 |
91.62 % |
413332044 |
93.55 % |
2779185 |
22.49 % |
| q20,qd2 |
19071609 |
4.20 % |
10417443 |
2.36 % |
8654166 |
70.04 % |
| q20,mq40 |
10347645 |
2.28 % |
10224044 |
2.31 % |
123601 |
1.00 % |
| qd2 |
3228570 |
0.71 % |
2864789 |
0.65 % |
363781 |
2.94 % |
| mq40 |
2704557 |
0.60 % |
2450723 |
0.55 % |
253834 |
2.05 % |
| q20,qd2,mq40 |
2653890 |
0.58 % |
2485705 |
0.56 % |
168185 |
1.36 % |
| qd2,mq40 |
61728 |
0.01 % |
50429 |
0.01 % |
11299 |
0.09 % |
| qd2,fs60,mq40 |
952 |
0.00 % |
0 |
0.00 % |
952 |
0.01 % |
| qd2,fs60 |
713 |
0.00 % |
0 |
0.00 % |
713 |
0.01 % |
| fs60 |
355 |
0.00 % |
0 |
0.00 % |
355 |
0.00 % |
| fs60,mq40 |
287 |
0.00 % |
0 |
0.00 % |
287 |
0.00 % |
| q20,qd2,fs60 |
175 |
0.00 % |
0 |
0.00 % |
175 |
0.00 % |
| q20,qd2,fs60,mq40 |
107 |
0.00 % |
0 |
0.00 % |
107 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
7728927 |
36.11 % |
| Transition |
G>A |
All |
993226 |
4.64 % |
| Transition |
T>C |
All |
6575230 |
30.72 % |
| Transition |
C>T |
All |
1057520 |
4.94 % |
| Transversion |
A>C |
All |
355152 |
1.66 % |
| Transversion |
C>A |
All |
1124943 |
5.26 % |
| Transversion |
T>G |
All |
414464 |
1.94 % |
| Transversion |
G>T |
All |
1075320 |
5.02 % |
| Transversion |
A>T |
All |
507803 |
2.37 % |
| Transversion |
T>A |
All |
555113 |
2.59 % |
| Transversion |
C>G |
All |
534567 |
2.50 % |
| Transversion |
G>C |
All |
483482 |
2.26 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
769603 |
21.57 % |
| Transition |
G>A |
Passed |
471350 |
13.21 % |
| Transition |
T>C |
Passed |
721803 |
20.23 % |
| Transition |
C>T |
Passed |
477720 |
13.39 % |
| Transversion |
A>C |
Passed |
134136 |
3.76 % |
| Transversion |
C>A |
Passed |
162210 |
4.55 % |
| Transversion |
T>G |
Passed |
136601 |
3.83 % |
| Transversion |
G>T |
Passed |
153559 |
4.30 % |
| Transversion |
A>T |
Passed |
131283 |
3.68 % |
| Transversion |
T>A |
Passed |
132613 |
3.72 % |
| Transversion |
C>G |
Passed |
139749 |
3.92 % |
| Transversion |
G>C |
Passed |
137027 |
3.84 % |
| |
|
|
|
|
| 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 |
16354903 |
5050844 |
| Passed |
2.17 |
2440476 |
1127178 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |