/EXTERNAL BLUEPRINT/variants/K006389_K006402_19_lane_gembs
BACK
SAMPLE K006389_K006402_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157446788 |
1049319169 |
90.66 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157446788 |
100% |
1147391107 |
99.13 % |
10055681 |
0.87 % |
| |
|
|
|
|
|
|
| Passed |
1050230673 |
90.74 % |
1046984127 |
91.25 % |
3246546 |
0.31 % |
| Filtered |
107216115 |
9.26 % |
100406980 |
8.75 % |
6809135 |
0.65 % |
| |
|
|
|
|
|
|
| q20 |
73935363 |
68.96 % |
73212695 |
72.92 % |
722668 |
10.61 % |
| q20,mq40 |
11342363 |
10.58 % |
11240668 |
11.20 % |
101695 |
1.49 % |
| q20,qd2 |
8523596 |
7.95 % |
3122537 |
3.11 % |
5401059 |
79.32 % |
| mq40 |
7094095 |
6.62 % |
6884314 |
6.86 % |
209781 |
3.08 % |
| qd2 |
3441823 |
3.21 % |
3290483 |
3.28 % |
151340 |
2.22 % |
| q20,qd2,mq40 |
2759667 |
2.57 % |
2562677 |
2.55 % |
196990 |
2.89 % |
| qd2,mq40 |
109711 |
0.10 % |
93606 |
0.09 % |
16105 |
0.24 % |
| fs60 |
2852 |
0.00 % |
0 |
0.00 % |
2852 |
0.04 % |
| q20,qd2,fs60 |
2202 |
0.00 % |
0 |
0.00 % |
2202 |
0.03 % |
| qd2,fs60 |
1715 |
0.00 % |
0 |
0.00 % |
1715 |
0.03 % |
| qd2,fs60,mq40 |
1660 |
0.00 % |
0 |
0.00 % |
1660 |
0.02 % |
| fs60,mq40 |
811 |
0.00 % |
0 |
0.00 % |
811 |
0.01 % |
| q20,qd2,fs60,mq40 |
250 |
0.00 % |
0 |
0.00 % |
250 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
3686391 |
31.22 % |
| Transition |
G>A |
All |
988865 |
8.37 % |
| Transition |
T>C |
All |
3662768 |
31.02 % |
| Transition |
C>T |
All |
990286 |
8.39 % |
| Transversion |
A>C |
All |
213641 |
1.81 % |
| Transversion |
C>A |
All |
476657 |
4.04 % |
| Transversion |
T>G |
All |
217954 |
1.85 % |
| Transversion |
G>T |
All |
471191 |
3.99 % |
| Transversion |
A>T |
All |
351894 |
2.98 % |
| Transversion |
T>A |
All |
346504 |
2.93 % |
| Transversion |
C>G |
All |
201493 |
1.71 % |
| Transversion |
G>C |
All |
200216 |
1.70 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
610244 |
17.25 % |
| Transition |
G>A |
Passed |
580725 |
16.42 % |
| Transition |
T>C |
Passed |
611951 |
17.30 % |
| Transition |
C>T |
Passed |
583132 |
16.49 % |
| Transversion |
A>C |
Passed |
149480 |
4.23 % |
| Transversion |
C>A |
Passed |
149112 |
4.22 % |
| Transversion |
T>G |
Passed |
150712 |
4.26 % |
| Transversion |
G>T |
Passed |
149097 |
4.22 % |
| Transversion |
A>T |
Passed |
127610 |
3.61 % |
| Transversion |
T>A |
Passed |
127957 |
3.62 % |
| Transversion |
C>G |
Passed |
148221 |
4.19 % |
| Transversion |
G>C |
Passed |
148923 |
4.21 % |
| |
|
|
|
|
| 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 |
3.76 |
9328310 |
2479550 |
| Passed |
2.07 |
2386052 |
1151112 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |