/EXTERNAL BLUEPRINT/variants/K011770_K011771_K011772_K011773_K011774_K011775_K011776_K011777_K011778_K011798_K011799_11_lane_gembs
BACK
SAMPLE K011770_K011771_K011772_K011773_K011774_K011775_K011776_K011777_K011778_K011798_K011799_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
940190370 |
11820540 |
1.26 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
940190370 |
100% |
918245427 |
97.67 % |
21944943 |
2.33 % |
| |
|
|
|
|
|
|
| Passed |
23319682 |
2.48 % |
11195898 |
1.22 % |
12123784 |
51.99 % |
| Filtered |
916870688 |
97.52 % |
907049529 |
98.78 % |
9821159 |
42.12 % |
| |
|
|
|
|
|
|
| q20 |
730308435 |
79.65 % |
723663943 |
79.78 % |
6644492 |
67.65 % |
| q20,qd2 |
113179209 |
12.34 % |
111107942 |
12.25 % |
2071267 |
21.09 % |
| q20,mq40 |
53683030 |
5.86 % |
53302328 |
5.88 % |
380702 |
3.88 % |
| q20,qd2,mq40 |
18898274 |
2.06 % |
18791300 |
2.07 % |
106974 |
1.09 % |
| mq40 |
792839 |
0.09 % |
175914 |
0.02 % |
616925 |
6.28 % |
| qd2 |
6900 |
0.00 % |
6523 |
0.00 % |
377 |
0.00 % |
| qd2,mq40 |
1955 |
0.00 % |
1579 |
0.00 % |
376 |
0.00 % |
| qd2,fs60 |
17 |
0.00 % |
0 |
0.00 % |
17 |
0.00 % |
| fs60,mq40 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
5991543 |
22.91 % |
| Transition |
G>A |
All |
2177878 |
8.33 % |
| Transition |
T>C |
All |
7450562 |
28.49 % |
| Transition |
C>T |
All |
973972 |
3.72 % |
| Transversion |
A>C |
All |
818667 |
3.13 % |
| Transversion |
C>A |
All |
1671602 |
6.39 % |
| Transversion |
T>G |
All |
997584 |
3.81 % |
| Transversion |
G>T |
All |
1494365 |
5.71 % |
| Transversion |
A>T |
All |
1153234 |
4.41 % |
| Transversion |
T>A |
All |
1640393 |
6.27 % |
| Transversion |
C>G |
All |
804462 |
3.08 % |
| Transversion |
G>C |
All |
977284 |
3.74 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
106123 |
17.05 % |
| Transition |
G>A |
Passed |
83086 |
13.35 % |
| Transition |
T>C |
Passed |
178057 |
28.61 % |
| Transition |
C>T |
Passed |
40922 |
6.58 % |
| Transversion |
A>C |
Passed |
25116 |
4.04 % |
| Transversion |
C>A |
Passed |
32261 |
5.18 % |
| Transversion |
T>G |
Passed |
26676 |
4.29 % |
| Transversion |
G>T |
Passed |
21251 |
3.41 % |
| Transversion |
A>T |
Passed |
13680 |
2.20 % |
| Transversion |
T>A |
Passed |
31075 |
4.99 % |
| Transversion |
C>G |
Passed |
27345 |
4.39 % |
| Transversion |
G>C |
Passed |
36764 |
5.91 % |
| |
|
|
|
|
| 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 |
1.74 |
16593955 |
9557591 |
| Passed |
1.91 |
408188 |
214168 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |