/EXTERNAL BLUEPRINT/variants/K006357_11_lane_gembs
BACK
SAMPLE K006357_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1120672803 |
673829756 |
60.13 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1120672803 |
100% |
1107713386 |
98.84 % |
12959417 |
1.16 % |
| |
|
|
|
|
|
|
| Passed |
675554207 |
60.28 % |
672389786 |
60.70 % |
3164421 |
0.47 % |
| Filtered |
445118596 |
39.72 % |
435323600 |
39.30 % |
9794996 |
1.45 % |
| |
|
|
|
|
|
|
| q20 |
384732511 |
86.43 % |
383195491 |
88.03 % |
1537020 |
15.69 % |
| q20,qd2 |
35915576 |
8.07 % |
28183876 |
6.47 % |
7731700 |
78.94 % |
| q20,mq40 |
13854363 |
3.11 % |
13755276 |
3.16 % |
99087 |
1.01 % |
| mq40 |
5821187 |
1.31 % |
5668939 |
1.30 % |
152248 |
1.55 % |
| q20,qd2,mq40 |
3091313 |
0.69 % |
2907123 |
0.67 % |
184190 |
1.88 % |
| qd2 |
1637025 |
0.37 % |
1559597 |
0.36 % |
77428 |
0.79 % |
| qd2,mq40 |
62166 |
0.01 % |
53298 |
0.01 % |
8868 |
0.09 % |
| q20,qd2,fs60 |
1368 |
0.00 % |
0 |
0.00 % |
1368 |
0.01 % |
| fs60 |
927 |
0.00 % |
0 |
0.00 % |
927 |
0.01 % |
| qd2,fs60,mq40 |
865 |
0.00 % |
0 |
0.00 % |
865 |
0.01 % |
| qd2,fs60 |
551 |
0.00 % |
0 |
0.00 % |
551 |
0.01 % |
| q20,qd2,fs60,mq40 |
380 |
0.00 % |
0 |
0.00 % |
380 |
0.00 % |
| fs60,mq40 |
361 |
0.00 % |
0 |
0.00 % |
361 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
3235205 |
21.82 % |
| Transition |
G>A |
All |
2801599 |
18.90 % |
| Transition |
T>C |
All |
3097849 |
20.90 % |
| Transition |
C>T |
All |
2694830 |
18.18 % |
| Transversion |
A>C |
All |
243359 |
1.64 % |
| Transversion |
C>A |
All |
563884 |
3.80 % |
| Transversion |
T>G |
All |
258007 |
1.74 % |
| Transversion |
G>T |
All |
557907 |
3.76 % |
| Transversion |
A>T |
All |
483286 |
3.26 % |
| Transversion |
T>A |
All |
481905 |
3.25 % |
| Transversion |
C>G |
All |
207232 |
1.40 % |
| Transversion |
G>C |
All |
199337 |
1.34 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
393464 |
18.49 % |
| Transition |
G>A |
Passed |
361754 |
17.00 % |
| Transition |
T>C |
Passed |
393316 |
18.48 % |
| Transition |
C>T |
Passed |
360969 |
16.96 % |
| Transversion |
A>C |
Passed |
82261 |
3.87 % |
| Transversion |
C>A |
Passed |
75682 |
3.56 % |
| Transversion |
T>G |
Passed |
82341 |
3.87 % |
| Transversion |
G>T |
Passed |
75678 |
3.56 % |
| Transversion |
A>T |
Passed |
53586 |
2.52 % |
| Transversion |
T>A |
Passed |
53641 |
2.52 % |
| Transversion |
C>G |
Passed |
97406 |
4.58 % |
| Transversion |
G>C |
Passed |
97862 |
4.60 % |
| |
|
|
|
|
| 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 |
3.95 |
11829483 |
2994917 |
| Passed |
2.44 |
1509503 |
618457 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |