/cemt/variants/K005714_0_lane_gembs
BACK
SAMPLE K005714_0_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1174626995 |
729395670 |
62.10 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1174626995 |
100% |
1152950927 |
98.15 % |
21676068 |
1.85 % |
| |
|
|
|
|
|
|
| Passed |
734571007 |
62.54 % |
726520725 |
63.01 % |
8050282 |
1.10 % |
| Filtered |
440055988 |
37.46 % |
426430202 |
36.99 % |
13625786 |
1.85 % |
| |
|
|
|
|
|
|
| q20 |
404477892 |
91.92 % |
401599127 |
94.18 % |
2878765 |
21.13 % |
| q20,qd2 |
18028605 |
4.10 % |
8149384 |
1.91 % |
9879221 |
72.50 % |
| q20,mq40 |
9838032 |
2.24 % |
9720409 |
2.28 % |
117623 |
0.86 % |
| qd2 |
2858296 |
0.65 % |
2512375 |
0.59 % |
345921 |
2.54 % |
| q20,qd2,mq40 |
2591963 |
0.59 % |
2442016 |
0.57 % |
149947 |
1.10 % |
| mq40 |
2206926 |
0.50 % |
1964592 |
0.46 % |
242334 |
1.78 % |
| qd2,mq40 |
51839 |
0.01 % |
42299 |
0.01 % |
9540 |
0.07 % |
| qd2,fs60,mq40 |
908 |
0.00 % |
0 |
0.00 % |
908 |
0.01 % |
| qd2,fs60 |
695 |
0.00 % |
0 |
0.00 % |
695 |
0.01 % |
| fs60 |
356 |
0.00 % |
0 |
0.00 % |
356 |
0.00 % |
| fs60,mq40 |
247 |
0.00 % |
0 |
0.00 % |
247 |
0.00 % |
| q20,qd2,fs60 |
135 |
0.00 % |
0 |
0.00 % |
135 |
0.00 % |
| q20,qd2,fs60,mq40 |
93 |
0.00 % |
0 |
0.00 % |
93 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
8574975 |
36.41 % |
| Transition |
G>A |
All |
1325235 |
5.63 % |
| Transition |
T>C |
All |
7487801 |
31.79 % |
| Transition |
C>T |
All |
1362850 |
5.79 % |
| Transversion |
A>C |
All |
407494 |
1.73 % |
| Transversion |
C>A |
All |
891542 |
3.79 % |
| Transversion |
T>G |
All |
475128 |
2.02 % |
| Transversion |
G>T |
All |
839929 |
3.57 % |
| Transversion |
A>T |
All |
558142 |
2.37 % |
| Transversion |
T>A |
All |
604406 |
2.57 % |
| Transversion |
C>G |
All |
542342 |
2.30 % |
| Transversion |
G>C |
All |
481495 |
2.04 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
815922 |
21.71 % |
| Transition |
G>A |
Passed |
501701 |
13.35 % |
| Transition |
T>C |
Passed |
766591 |
20.39 % |
| Transition |
C>T |
Passed |
505041 |
13.44 % |
| Transversion |
A>C |
Passed |
143564 |
3.82 % |
| Transversion |
C>A |
Passed |
158481 |
4.22 % |
| Transversion |
T>G |
Passed |
147374 |
3.92 % |
| Transversion |
G>T |
Passed |
150754 |
4.01 % |
| Transversion |
A>T |
Passed |
136953 |
3.64 % |
| Transversion |
T>A |
Passed |
140624 |
3.74 % |
| Transversion |
C>G |
Passed |
147521 |
3.92 % |
| Transversion |
G>C |
Passed |
144551 |
3.85 % |
| |
|
|
|
|
| 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 |
3.91 |
18750861 |
4800478 |
| Passed |
2.21 |
2589255 |
1169822 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |