/EXTERNAL BLUEPRINT/variants/K006430_22_lane_gembs
BACK
SAMPLE K006430_22_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156816600 |
934209218 |
80.76 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156816600 |
100% |
1143307153 |
98.83 % |
13509447 |
1.17 % |
| |
|
|
|
|
|
|
| Passed |
936308507 |
80.94 % |
931986255 |
81.52 % |
4322252 |
0.46 % |
| Filtered |
220508093 |
19.06 % |
211320898 |
18.48 % |
9187195 |
0.98 % |
| |
|
|
|
|
|
|
| q20 |
183684561 |
83.30 % |
182395713 |
86.31 % |
1288848 |
14.03 % |
| q20,mq40 |
13814747 |
6.26 % |
13708071 |
6.49 % |
106676 |
1.16 % |
| q20,qd2 |
12963706 |
5.88 % |
5619701 |
2.66 % |
7344005 |
79.94 % |
| mq40 |
4677907 |
2.12 % |
4489577 |
2.12 % |
188330 |
2.05 % |
| q20,qd2,mq40 |
3002145 |
1.36 % |
2828528 |
1.34 % |
173617 |
1.89 % |
| qd2 |
2318349 |
1.05 % |
2241982 |
1.06 % |
76367 |
0.83 % |
| qd2,mq40 |
45200 |
0.02 % |
37326 |
0.02 % |
7874 |
0.09 % |
| qd2,fs60,mq40 |
614 |
0.00 % |
0 |
0.00 % |
614 |
0.01 % |
| fs60,mq40 |
298 |
0.00 % |
0 |
0.00 % |
298 |
0.00 % |
| qd2,fs60 |
211 |
0.00 % |
0 |
0.00 % |
211 |
0.00 % |
| fs60 |
208 |
0.00 % |
0 |
0.00 % |
208 |
0.00 % |
| q20,qd2,fs60,mq40 |
96 |
0.00 % |
0 |
0.00 % |
96 |
0.00 % |
| q20,qd2,fs60 |
49 |
0.00 % |
0 |
0.00 % |
49 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
5018855 |
33.03 % |
| Transition |
G>A |
All |
1072702 |
7.06 % |
| Transition |
T>C |
All |
4971656 |
32.72 % |
| Transition |
C>T |
All |
1081905 |
7.12 % |
| Transversion |
A>C |
All |
233120 |
1.53 % |
| Transversion |
C>A |
All |
654348 |
4.31 % |
| Transversion |
T>G |
All |
236578 |
1.56 % |
| Transversion |
G>T |
All |
650251 |
4.28 % |
| Transversion |
A>T |
All |
430967 |
2.84 % |
| Transversion |
T>A |
All |
424467 |
2.79 % |
| Transversion |
C>G |
All |
210925 |
1.39 % |
| Transversion |
G>C |
All |
209996 |
1.38 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
556859 |
17.24 % |
| Transition |
G>A |
Passed |
527854 |
16.34 % |
| Transition |
T>C |
Passed |
557545 |
17.26 % |
| Transition |
C>T |
Passed |
531527 |
16.45 % |
| Transversion |
A>C |
Passed |
135855 |
4.20 % |
| Transversion |
C>A |
Passed |
138168 |
4.28 % |
| Transversion |
T>G |
Passed |
136609 |
4.23 % |
| Transversion |
G>T |
Passed |
138462 |
4.29 % |
| Transversion |
A>T |
Passed |
112249 |
3.47 % |
| Transversion |
T>A |
Passed |
112787 |
3.49 % |
| Transversion |
C>G |
Passed |
141063 |
4.37 % |
| Transversion |
G>C |
Passed |
141922 |
4.39 % |
| |
|
|
|
|
| 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 |
3.98 |
12145118 |
3050652 |
| Passed |
2.06 |
2173785 |
1057115 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |