/EXTERNAL BLUEPRINT/variants/K006321_8_lane_gembs
BACK
SAMPLE K006321_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1101800494 |
221652701 |
20.12 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1101800494 |
100% |
1075988130 |
97.66 % |
25812364 |
2.34 % |
| |
|
|
|
|
|
|
| Passed |
229463727 |
20.83 % |
220620220 |
20.50 % |
8843507 |
3.85 % |
| Filtered |
872336767 |
79.17 % |
855367910 |
79.50 % |
16968857 |
7.40 % |
| |
|
|
|
|
|
|
| q20 |
790716580 |
90.64 % |
784094309 |
91.67 % |
6622271 |
39.03 % |
| q20,qd2 |
63521280 |
7.28 % |
53443027 |
6.25 % |
10078253 |
59.39 % |
| q20,mq40 |
12231210 |
1.40 % |
12142870 |
1.42 % |
88340 |
0.52 % |
| q20,qd2,mq40 |
5426146 |
0.62 % |
5365069 |
0.63 % |
61077 |
0.36 % |
| mq40 |
324338 |
0.04 % |
218857 |
0.03 % |
105481 |
0.62 % |
| qd2 |
102769 |
0.01 % |
92054 |
0.01 % |
10715 |
0.06 % |
| qd2,mq40 |
14053 |
0.00 % |
11724 |
0.00 % |
2329 |
0.01 % |
| qd2,fs60,mq40 |
199 |
0.00 % |
0 |
0.00 % |
199 |
0.00 % |
| fs60,mq40 |
74 |
0.00 % |
0 |
0.00 % |
74 |
0.00 % |
| qd2,fs60 |
68 |
0.00 % |
0 |
0.00 % |
68 |
0.00 % |
| q20,qd2,fs60,mq40 |
33 |
0.00 % |
0 |
0.00 % |
33 |
0.00 % |
| fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| q20,qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
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 |
8559419 |
30.73 % |
| Transition |
G>A |
All |
1224981 |
4.40 % |
| Transition |
T>C |
All |
8600981 |
30.88 % |
| Transition |
C>T |
All |
1226797 |
4.40 % |
| Transversion |
A>C |
All |
429693 |
1.54 % |
| Transversion |
C>A |
All |
1474876 |
5.29 % |
| Transversion |
T>G |
All |
426843 |
1.53 % |
| Transversion |
G>T |
All |
1467518 |
5.27 % |
| Transversion |
A>T |
All |
1902842 |
6.83 % |
| Transversion |
T>A |
All |
1910917 |
6.86 % |
| Transversion |
C>G |
All |
315222 |
1.13 % |
| Transversion |
G>C |
All |
317164 |
1.14 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
239817 |
18.91 % |
| Transition |
G>A |
Passed |
185285 |
14.61 % |
| Transition |
T>C |
Passed |
239340 |
18.87 % |
| Transition |
C>T |
Passed |
186841 |
14.73 % |
| Transversion |
A>C |
Passed |
51505 |
4.06 % |
| Transversion |
C>A |
Passed |
55990 |
4.42 % |
| Transversion |
T>G |
Passed |
51660 |
4.07 % |
| Transversion |
G>T |
Passed |
55478 |
4.37 % |
| Transversion |
A>T |
Passed |
51883 |
4.09 % |
| Transversion |
T>A |
Passed |
53235 |
4.20 % |
| Transversion |
C>G |
Passed |
48588 |
3.83 % |
| Transversion |
G>C |
Passed |
48450 |
3.82 % |
| |
|
|
|
|
| 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 |
2.38 |
19612178 |
8245075 |
| Passed |
2.04 |
851283 |
416789 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |