/EXTERNAL BLUEPRINT/variants/K006273_11_lane_gembs
BACK
SAMPLE K006273_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1123680021 |
650982456 |
57.93 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1123680021 |
100% |
1105354021 |
98.37 % |
18326000 |
1.63 % |
| |
|
|
|
|
|
|
| Passed |
653032967 |
58.12 % |
649182798 |
58.73 % |
3850169 |
0.59 % |
| Filtered |
470647054 |
41.88 % |
456171223 |
41.27 % |
14475831 |
2.22 % |
| |
|
|
|
|
|
|
| q20 |
397774837 |
84.52 % |
395888434 |
86.79 % |
1886403 |
13.03 % |
| q20,qd2 |
45157416 |
9.59 % |
33184828 |
7.27 % |
11972588 |
82.71 % |
| q20,mq40 |
15138202 |
3.22 % |
15031659 |
3.30 % |
106543 |
0.74 % |
| mq40 |
6826667 |
1.45 % |
6635152 |
1.45 % |
191515 |
1.32 % |
| q20,qd2,mq40 |
3334957 |
0.71 % |
3149933 |
0.69 % |
185024 |
1.28 % |
| qd2 |
2319322 |
0.49 % |
2204580 |
0.48 % |
114742 |
0.79 % |
| qd2,mq40 |
88236 |
0.02 % |
76637 |
0.02 % |
11599 |
0.08 % |
| q20,qd2,fs60 |
1980 |
0.00 % |
0 |
0.00 % |
1980 |
0.01 % |
| qd2,fs60,mq40 |
1525 |
0.00 % |
0 |
0.00 % |
1525 |
0.01 % |
| fs60 |
1475 |
0.00 % |
0 |
0.00 % |
1475 |
0.01 % |
| qd2,fs60 |
1245 |
0.00 % |
0 |
0.00 % |
1245 |
0.01 % |
| q20,qd2,fs60,mq40 |
634 |
0.00 % |
0 |
0.00 % |
634 |
0.00 % |
| fs60,mq40 |
557 |
0.00 % |
0 |
0.00 % |
557 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3636020 |
16.15 % |
| Transition |
G>A |
All |
6085860 |
27.03 % |
| Transition |
T>C |
All |
3514254 |
15.61 % |
| Transition |
C>T |
All |
5915352 |
26.27 % |
| Transversion |
A>C |
All |
250602 |
1.11 % |
| Transversion |
C>A |
All |
659029 |
2.93 % |
| Transversion |
T>G |
All |
263468 |
1.17 % |
| Transversion |
G>T |
All |
636962 |
2.83 % |
| Transversion |
A>T |
All |
544508 |
2.42 % |
| Transversion |
T>A |
All |
554030 |
2.46 % |
| Transversion |
C>G |
All |
232187 |
1.03 % |
| Transversion |
G>C |
All |
223685 |
0.99 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
475923 |
18.92 % |
| Transition |
G>A |
Passed |
428448 |
17.03 % |
| Transition |
T>C |
Passed |
473331 |
18.82 % |
| Transition |
C>T |
Passed |
427476 |
16.99 % |
| Transversion |
A>C |
Passed |
92125 |
3.66 % |
| Transversion |
C>A |
Passed |
88414 |
3.51 % |
| Transversion |
T>G |
Passed |
92044 |
3.66 % |
| Transversion |
G>T |
Passed |
88093 |
3.50 % |
| Transversion |
A>T |
Passed |
62304 |
2.48 % |
| Transversion |
T>A |
Passed |
62857 |
2.50 % |
| Transversion |
C>G |
Passed |
112133 |
4.46 % |
| Transversion |
G>C |
Passed |
112222 |
4.46 % |
| |
|
|
|
|
| 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 |
5.69 |
19151486 |
3364471 |
| Passed |
2.54 |
1805178 |
710192 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |