/EXTERNAL BLUEPRINT/variants/K006264_19_lane_gembs
BACK
SAMPLE K006264_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1134232922 |
777808272 |
68.58 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1134232922 |
100% |
1115134120 |
98.32 % |
19098802 |
1.68 % |
| |
|
|
|
|
|
|
| Passed |
779027080 |
68.68 % |
776236391 |
69.61 % |
2790689 |
0.36 % |
| Filtered |
355205842 |
31.32 % |
338897729 |
30.39 % |
16308113 |
2.09 % |
| |
|
|
|
|
|
|
| q20 |
283277258 |
79.75 % |
281780245 |
83.15 % |
1497013 |
9.18 % |
| q20,qd2 |
39646418 |
11.16 % |
25535016 |
7.53 % |
14111402 |
86.53 % |
| q20,mq40 |
15380705 |
4.33 % |
15261094 |
4.50 % |
119611 |
0.73 % |
| mq40 |
10749775 |
3.03 % |
10543749 |
3.11 % |
206026 |
1.26 % |
| q20,qd2,mq40 |
3218085 |
0.91 % |
2987756 |
0.88 % |
230329 |
1.41 % |
| qd2 |
2793672 |
0.79 % |
2678502 |
0.79 % |
115170 |
0.71 % |
| qd2,mq40 |
126725 |
0.04 % |
111367 |
0.03 % |
15358 |
0.09 % |
| q20,qd2,fs60 |
5777 |
0.00 % |
0 |
0.00 % |
5777 |
0.04 % |
| fs60 |
2356 |
0.00 % |
0 |
0.00 % |
2356 |
0.01 % |
| qd2,fs60,mq40 |
1980 |
0.00 % |
0 |
0.00 % |
1980 |
0.01 % |
| qd2,fs60 |
1577 |
0.00 % |
0 |
0.00 % |
1577 |
0.01 % |
| fs60,mq40 |
848 |
0.00 % |
0 |
0.00 % |
848 |
0.01 % |
| q20,qd2,fs60,mq40 |
659 |
0.00 % |
0 |
0.00 % |
659 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
2755010 |
10.01 % |
| Transition |
G>A |
All |
9840061 |
35.77 % |
| Transition |
T>C |
All |
2617574 |
9.51 % |
| Transition |
C>T |
All |
9666066 |
35.13 % |
| Transversion |
A>C |
All |
206934 |
0.75 % |
| Transversion |
C>A |
All |
513791 |
1.87 % |
| Transversion |
T>G |
All |
216673 |
0.79 % |
| Transversion |
G>T |
All |
511696 |
1.86 % |
| Transversion |
A>T |
All |
405709 |
1.47 % |
| Transversion |
T>A |
All |
395892 |
1.44 % |
| Transversion |
C>G |
All |
194906 |
0.71 % |
| Transversion |
G>C |
All |
187502 |
0.68 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
431231 |
18.15 % |
| Transition |
G>A |
Passed |
408721 |
17.21 % |
| Transition |
T>C |
Passed |
434217 |
18.28 % |
| Transition |
C>T |
Passed |
409289 |
17.23 % |
| Transversion |
A>C |
Passed |
90862 |
3.83 % |
| Transversion |
C>A |
Passed |
86535 |
3.64 % |
| Transversion |
T>G |
Passed |
90348 |
3.80 % |
| Transversion |
G>T |
Passed |
86199 |
3.63 % |
| Transversion |
A>T |
Passed |
63671 |
2.68 % |
| Transversion |
T>A |
Passed |
64204 |
2.70 % |
| Transversion |
C>G |
Passed |
104797 |
4.41 % |
| Transversion |
G>C |
Passed |
105292 |
4.43 % |
| |
|
|
|
|
| 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 |
9.45 |
24878711 |
2633103 |
| Passed |
2.43 |
1683458 |
691908 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |