/EXTERNAL Roadmap/variants/K012799_1_lane_gembs
BACK
SAMPLE K012799_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1162649920 |
954594352 |
82.11 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1162649920 |
100% |
1142861749 |
98.30 % |
19788171 |
1.70 % |
| |
|
|
|
|
|
|
| Passed |
956514119 |
82.27 % |
951338309 |
83.24 % |
5175810 |
0.54 % |
| Filtered |
206135801 |
17.73 % |
191523440 |
16.76 % |
14612361 |
1.53 % |
| |
|
|
|
|
|
|
| q20 |
162494104 |
78.83 % |
160690723 |
83.90 % |
1803381 |
12.34 % |
| q20,qd2 |
18319428 |
8.89 % |
6358784 |
3.32 % |
11960644 |
81.85 % |
| q20,mq40 |
15298709 |
7.42 % |
15142175 |
7.91 % |
156534 |
1.07 % |
| mq40 |
3787148 |
1.84 % |
3510508 |
1.83 % |
276640 |
1.89 % |
| q20,qd2,mq40 |
3473162 |
1.68 % |
3270595 |
1.71 % |
202567 |
1.39 % |
| qd2 |
2714925 |
1.32 % |
2512140 |
1.31 % |
202785 |
1.39 % |
| qd2,mq40 |
47271 |
0.02 % |
38515 |
0.02 % |
8756 |
0.06 % |
| qd2,fs60,mq40 |
533 |
0.00 % |
0 |
0.00 % |
533 |
0.00 % |
| fs60,mq40 |
243 |
0.00 % |
0 |
0.00 % |
243 |
0.00 % |
| qd2,fs60 |
164 |
0.00 % |
0 |
0.00 % |
164 |
0.00 % |
| fs60 |
51 |
0.00 % |
0 |
0.00 % |
51 |
0.00 % |
| q20,qd2,fs60,mq40 |
47 |
0.00 % |
0 |
0.00 % |
47 |
0.00 % |
| q20,qd2,fs60 |
15 |
0.00 % |
0 |
0.00 % |
15 |
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 |
8253664 |
38.31 % |
| Transition |
G>A |
All |
1542415 |
7.16 % |
| Transition |
T>C |
All |
6465072 |
30.01 % |
| Transition |
C>T |
All |
1703745 |
7.91 % |
| Transversion |
A>C |
All |
270293 |
1.25 % |
| Transversion |
C>A |
All |
658767 |
3.06 % |
| Transversion |
T>G |
All |
323172 |
1.50 % |
| Transversion |
G>T |
All |
616147 |
2.86 % |
| Transversion |
A>T |
All |
540188 |
2.51 % |
| Transversion |
T>A |
All |
575176 |
2.67 % |
| Transversion |
C>G |
All |
321343 |
1.49 % |
| Transversion |
G>C |
All |
274199 |
1.27 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
869956 |
19.97 % |
| Transition |
G>A |
Passed |
675823 |
15.51 % |
| Transition |
T>C |
Passed |
748460 |
17.18 % |
| Transition |
C>T |
Passed |
687332 |
15.78 % |
| Transversion |
A>C |
Passed |
171190 |
3.93 % |
| Transversion |
C>A |
Passed |
180829 |
4.15 % |
| Transversion |
T>G |
Passed |
173939 |
3.99 % |
| Transversion |
G>T |
Passed |
181288 |
4.16 % |
| Transversion |
A>T |
Passed |
157198 |
3.61 % |
| Transversion |
T>A |
Passed |
157635 |
3.62 % |
| Transversion |
C>G |
Passed |
177311 |
4.07 % |
| Transversion |
G>C |
Passed |
175348 |
4.03 % |
| |
|
|
|
|
| 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 |
5.02 |
17964896 |
3579285 |
| Passed |
2.17 |
2981571 |
1374738 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |