/CEMT/variants/A77955_1_lane_gembs
BACK
SAMPLE A77955_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1177941100 |
977282957 |
82.97 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1177941100 |
100% |
1155590352 |
98.10 % |
22350748 |
1.90 % |
| |
|
|
|
|
|
|
| Passed |
980575462 |
83.24 % |
973804738 |
84.27 % |
6770724 |
0.69 % |
| Filtered |
197365638 |
16.76 % |
181785614 |
15.73 % |
15580024 |
1.59 % |
| |
|
|
|
|
|
|
| q20 |
161857051 |
82.01 % |
160529815 |
88.31 % |
1327236 |
8.52 % |
| q20,qd2 |
18387806 |
9.32 % |
5167804 |
2.84 % |
13220002 |
84.85 % |
| q20,mq40 |
10096159 |
5.12 % |
9983554 |
5.49 % |
112605 |
0.72 % |
| q20,qd2,mq40 |
2492916 |
1.26 % |
2349181 |
1.29 % |
143735 |
0.92 % |
| qd2 |
2301175 |
1.17 % |
1794646 |
0.99 % |
506529 |
3.25 % |
| mq40 |
2184697 |
1.11 % |
1925247 |
1.06 % |
259450 |
1.67 % |
| qd2,mq40 |
44508 |
0.02 % |
35367 |
0.02 % |
9141 |
0.06 % |
| qd2,fs60,mq40 |
606 |
0.00 % |
0 |
0.00 % |
606 |
0.00 % |
| qd2,fs60 |
265 |
0.00 % |
0 |
0.00 % |
265 |
0.00 % |
| fs60,mq40 |
260 |
0.00 % |
0 |
0.00 % |
260 |
0.00 % |
| fs60 |
121 |
0.00 % |
0 |
0.00 % |
121 |
0.00 % |
| q20,qd2,fs60,mq40 |
52 |
0.00 % |
0 |
0.00 % |
52 |
0.00 % |
| q20,qd2,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
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 |
8818351 |
36.58 % |
| Transition |
G>A |
All |
965844 |
4.01 % |
| Transition |
T>C |
All |
8784537 |
36.44 % |
| Transition |
C>T |
All |
969029 |
4.02 % |
| Transversion |
A>C |
All |
421104 |
1.75 % |
| Transversion |
C>A |
All |
1054602 |
4.37 % |
| Transversion |
T>G |
All |
418823 |
1.74 % |
| Transversion |
G>T |
All |
874234 |
3.63 % |
| Transversion |
A>T |
All |
521074 |
2.16 % |
| Transversion |
T>A |
All |
547447 |
2.27 % |
| Transversion |
C>G |
All |
369742 |
1.53 % |
| Transversion |
G>C |
All |
361517 |
1.50 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
880047 |
18.85 % |
| Transition |
G>A |
Passed |
585684 |
12.55 % |
| Transition |
T>C |
Passed |
919353 |
19.69 % |
| Transition |
C>T |
Passed |
585841 |
12.55 % |
| Transversion |
A>C |
Passed |
181966 |
3.90 % |
| Transversion |
C>A |
Passed |
365965 |
7.84 % |
| Transversion |
T>G |
Passed |
183907 |
3.94 % |
| Transversion |
G>T |
Passed |
299521 |
6.42 % |
| Transversion |
A>T |
Passed |
163068 |
3.49 % |
| Transversion |
T>A |
Passed |
171665 |
3.68 % |
| Transversion |
C>G |
Passed |
166245 |
3.56 % |
| Transversion |
G>C |
Passed |
164818 |
3.53 % |
| |
|
|
|
|
| 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 |
4.28 |
19537761 |
4568543 |
| Passed |
1.75 |
2970925 |
1697155 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |