/EXTERNAL BLUEPRINT/variants/K011727_K011729_K011730_K011731_K011732_K011733_K011734_K011735_K011736_K011766_K011767_11_lane_gembs
BACK
SAMPLE K011727_K011729_K011730_K011731_K011732_K011733_K011734_K011735_K011736_K011766_K011767_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1012998947 |
26723474 |
2.64 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1012998947 |
100% |
982243909 |
96.96 % |
30755038 |
3.04 % |
| |
|
|
|
|
|
|
| Passed |
39882231 |
3.94 % |
25578196 |
2.60 % |
14304035 |
35.87 % |
| Filtered |
973116716 |
96.06 % |
956665713 |
97.40 % |
16451003 |
41.25 % |
| |
|
|
|
|
|
|
| q20 |
784063010 |
80.57 % |
773229799 |
80.83 % |
10833211 |
65.85 % |
| q20,qd2 |
103687553 |
10.66 % |
99750062 |
10.43 % |
3937491 |
23.93 % |
| q20,mq40 |
62929129 |
6.47 % |
62259382 |
6.51 % |
669747 |
4.07 % |
| q20,qd2,mq40 |
21166721 |
2.18 % |
20979774 |
2.19 % |
186947 |
1.14 % |
| mq40 |
1256863 |
0.13 % |
435417 |
0.05 % |
821446 |
4.99 % |
| qd2 |
9779 |
0.00 % |
8430 |
0.00 % |
1349 |
0.01 % |
| qd2,mq40 |
3596 |
0.00 % |
2849 |
0.00 % |
747 |
0.00 % |
| fs60,mq40 |
25 |
0.00 % |
0 |
0.00 % |
25 |
0.00 % |
| qd2,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| qd2,fs60,mq40 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,qd2,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
7793760 |
22.40 % |
| Transition |
G>A |
All |
2850877 |
8.19 % |
| Transition |
T>C |
All |
9826107 |
28.24 % |
| Transition |
C>T |
All |
1229780 |
3.53 % |
| Transversion |
A>C |
All |
1102026 |
3.17 % |
| Transversion |
C>A |
All |
2342379 |
6.73 % |
| Transversion |
T>G |
All |
1394065 |
4.01 % |
| Transversion |
G>T |
All |
2035359 |
5.85 % |
| Transversion |
A>T |
All |
1559167 |
4.48 % |
| Transversion |
T>A |
All |
2238522 |
6.43 % |
| Transversion |
C>G |
All |
1132225 |
3.25 % |
| Transversion |
G>C |
All |
1285118 |
3.69 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
202439 |
17.62 % |
| Transition |
G>A |
Passed |
153696 |
13.37 % |
| Transition |
T>C |
Passed |
349717 |
30.43 % |
| Transition |
C>T |
Passed |
60576 |
5.27 % |
| Transversion |
A>C |
Passed |
41659 |
3.63 % |
| Transversion |
C>A |
Passed |
65936 |
5.74 % |
| Transversion |
T>G |
Passed |
48762 |
4.24 % |
| Transversion |
G>T |
Passed |
33214 |
2.89 % |
| Transversion |
A>T |
Passed |
22609 |
1.97 % |
| Transversion |
T>A |
Passed |
65606 |
5.71 % |
| Transversion |
C>G |
Passed |
45176 |
3.93 % |
| Transversion |
G>C |
Passed |
59816 |
5.20 % |
| |
|
|
|
|
| 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 |
1.66 |
21700524 |
13088861 |
| Passed |
2.00 |
766428 |
382778 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |