/EXTERNAL BLUEPRINT/variants/K006370_15_lane_gembs
BACK
SAMPLE K006370_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
998896004 |
380396048 |
38.08 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
998896004 |
100% |
984249450 |
98.53 % |
14646554 |
1.47 % |
| |
|
|
|
|
|
|
| Passed |
382159186 |
38.26 % |
379648057 |
38.57 % |
2511129 |
0.66 % |
| Filtered |
616736818 |
61.74 % |
604601393 |
61.43 % |
12135425 |
3.18 % |
| |
|
|
|
|
|
|
| q20 |
498817725 |
80.88 % |
496923311 |
82.19 % |
1894414 |
15.61 % |
| q20,qd2 |
79660632 |
12.92 % |
69913692 |
11.56 % |
9746940 |
80.32 % |
| q20,mq40 |
18786035 |
3.05 % |
18683511 |
3.09 % |
102524 |
0.84 % |
| qd2 |
9406149 |
1.53 % |
9332614 |
1.54 % |
73535 |
0.61 % |
| mq40 |
5533728 |
0.90 % |
5395935 |
0.89 % |
137793 |
1.14 % |
| q20,qd2,mq40 |
4430507 |
0.72 % |
4275890 |
0.71 % |
154617 |
1.27 % |
| qd2,mq40 |
87143 |
0.01 % |
76440 |
0.01 % |
10703 |
0.09 % |
| q20,qd2,fs60 |
4907 |
0.00 % |
0 |
0.00 % |
4907 |
0.04 % |
| qd2,fs60 |
4262 |
0.00 % |
0 |
0.00 % |
4262 |
0.04 % |
| fs60 |
2249 |
0.00 % |
0 |
0.00 % |
2249 |
0.02 % |
| qd2,fs60,mq40 |
1971 |
0.00 % |
0 |
0.00 % |
1971 |
0.02 % |
| q20,qd2,fs60,mq40 |
947 |
0.00 % |
0 |
0.00 % |
947 |
0.01 % |
| fs60,mq40 |
560 |
0.00 % |
0 |
0.00 % |
560 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
2742175 |
11.29 % |
| Transition |
G>A |
All |
8169479 |
33.62 % |
| Transition |
T>C |
All |
2468996 |
10.16 % |
| Transition |
C>T |
All |
8039002 |
33.08 % |
| Transversion |
A>C |
All |
231583 |
0.95 % |
| Transversion |
C>A |
All |
545763 |
2.25 % |
| Transversion |
T>G |
All |
262548 |
1.08 % |
| Transversion |
G>T |
All |
530332 |
2.18 % |
| Transversion |
A>T |
All |
437387 |
1.80 % |
| Transversion |
T>A |
All |
450084 |
1.85 % |
| Transversion |
C>G |
All |
218282 |
0.90 % |
| Transversion |
G>C |
All |
202690 |
0.83 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
221140 |
20.00 % |
| Transition |
G>A |
Passed |
191820 |
17.35 % |
| Transition |
T>C |
Passed |
221126 |
20.00 % |
| Transition |
C>T |
Passed |
190954 |
17.27 % |
| Transversion |
A>C |
Passed |
37692 |
3.41 % |
| Transversion |
C>A |
Passed |
31635 |
2.86 % |
| Transversion |
T>G |
Passed |
37681 |
3.41 % |
| Transversion |
G>T |
Passed |
31790 |
2.87 % |
| Transversion |
A>T |
Passed |
18943 |
1.71 % |
| Transversion |
T>A |
Passed |
18708 |
1.69 % |
| Transversion |
C>G |
Passed |
52046 |
4.71 % |
| Transversion |
G>C |
Passed |
52257 |
4.73 % |
| |
|
|
|
|
| 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 |
7.44 |
21419652 |
2878669 |
| Passed |
2.94 |
825040 |
280752 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |