/EXTERNAL BLUEPRINT/variants/K012120_K012121_K012122_K012123_K012124_K012125_K012126_K012127_K012128_9_lane_gembs
BACK
SAMPLE K012120_K012121_K012122_K012123_K012124_K012125_K012126_K012127_K012128_9_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
855500067 |
2634184 |
0.31 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
855500067 |
100% |
840808474 |
98.28 % |
14691593 |
1.72 % |
| |
|
|
|
|
|
|
| Passed |
10914376 |
1.28 % |
2242527 |
0.27 % |
8671849 |
79.45 % |
| Filtered |
844585691 |
98.72 % |
838565947 |
99.73 % |
6019744 |
55.15 % |
| |
|
|
|
|
|
|
| q20 |
668946202 |
79.20 % |
664676874 |
79.26 % |
4269328 |
70.92 % |
| q20,qd2 |
108820695 |
12.88 % |
107828491 |
12.86 % |
992204 |
16.48 % |
| q20,mq40 |
49932551 |
5.91 % |
49658820 |
5.92 % |
273731 |
4.55 % |
| q20,qd2,mq40 |
16384141 |
1.94 % |
16326464 |
1.95 % |
57677 |
0.96 % |
| mq40 |
495332 |
0.06 % |
69025 |
0.01 % |
426307 |
7.08 % |
| qd2 |
5452 |
0.00 % |
5289 |
0.00 % |
163 |
0.00 % |
| qd2,mq40 |
1264 |
0.00 % |
984 |
0.00 % |
280 |
0.00 % |
| fs60,mq40 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| qd2,fs60 |
16 |
0.00 % |
0 |
0.00 % |
16 |
0.00 % |
| fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| qd2,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 % |
| 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 |
4215636 |
21.59 % |
| Transition |
G>A |
All |
1499962 |
7.68 % |
| Transition |
T>C |
All |
5594290 |
28.65 % |
| Transition |
C>T |
All |
743180 |
3.81 % |
| Transversion |
A>C |
All |
718346 |
3.68 % |
| Transversion |
C>A |
All |
1211752 |
6.21 % |
| Transversion |
T>G |
All |
786889 |
4.03 % |
| Transversion |
G>T |
All |
1126427 |
5.77 % |
| Transversion |
A>T |
All |
893393 |
4.58 % |
| Transversion |
T>A |
All |
1209929 |
6.20 % |
| Transversion |
C>G |
All |
700969 |
3.59 % |
| Transversion |
G>C |
All |
824573 |
4.22 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
60180 |
15.50 % |
| Transition |
G>A |
Passed |
48183 |
12.41 % |
| Transition |
T>C |
Passed |
102606 |
26.42 % |
| Transition |
C>T |
Passed |
21922 |
5.64 % |
| Transversion |
A>C |
Passed |
18227 |
4.69 % |
| Transversion |
C>A |
Passed |
23247 |
5.99 % |
| Transversion |
T>G |
Passed |
18427 |
4.74 % |
| Transversion |
G>T |
Passed |
15824 |
4.07 % |
| Transversion |
A>T |
Passed |
10330 |
2.66 % |
| Transversion |
T>A |
Passed |
22574 |
5.81 % |
| Transversion |
C>G |
Passed |
19648 |
5.06 % |
| Transversion |
G>C |
Passed |
27200 |
7.00 % |
| |
|
|
|
|
| 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 |
1.61 |
12053068 |
7472278 |
| Passed |
1.50 |
232891 |
155477 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |