/EXTERNAL BLUEPRINT/variants/K006337_6_lane_gembs
BACK
SAMPLE K006337_6_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1140918016 |
842231678 |
73.82 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1140918016 |
100% |
1121591821 |
98.31 % |
19326195 |
1.69 % |
| |
|
|
|
|
|
|
| Passed |
843682274 |
73.95 % |
840428239 |
74.93 % |
3254035 |
0.39 % |
| Filtered |
297235742 |
26.05 % |
281163582 |
25.07 % |
16072160 |
1.91 % |
| |
|
|
|
|
|
|
| q20 |
236956057 |
79.72 % |
235389637 |
83.72 % |
1566420 |
9.75 % |
| q20,qd2 |
33729647 |
11.35 % |
19924652 |
7.09 % |
13804995 |
85.89 % |
| q20,mq40 |
12161932 |
4.09 % |
12049023 |
4.29 % |
112909 |
0.70 % |
| mq40 |
8708140 |
2.93 % |
8511360 |
3.03 % |
196780 |
1.22 % |
| qd2 |
2806640 |
0.94 % |
2670939 |
0.95 % |
135701 |
0.84 % |
| q20,qd2,mq40 |
2736887 |
0.92 % |
2510542 |
0.89 % |
226345 |
1.41 % |
| qd2,mq40 |
123447 |
0.04 % |
107429 |
0.04 % |
16018 |
0.10 % |
| q20,qd2,fs60 |
5977 |
0.00 % |
0 |
0.00 % |
5977 |
0.04 % |
| fs60 |
2322 |
0.00 % |
0 |
0.00 % |
2322 |
0.01 % |
| qd2,fs60,mq40 |
1784 |
0.00 % |
0 |
0.00 % |
1784 |
0.01 % |
| qd2,fs60 |
1423 |
0.00 % |
0 |
0.00 % |
1423 |
0.01 % |
| fs60,mq40 |
787 |
0.00 % |
0 |
0.00 % |
787 |
0.00 % |
| q20,qd2,fs60,mq40 |
687 |
0.00 % |
0 |
0.00 % |
687 |
0.00 % |
| q20,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
3292034 |
13.28 % |
| Transition |
G>A |
All |
7887301 |
31.83 % |
| Transition |
T>C |
All |
3072422 |
12.40 % |
| Transition |
C>T |
All |
7770613 |
31.35 % |
| Transversion |
A>C |
All |
226064 |
0.91 % |
| Transversion |
C>A |
All |
539288 |
2.18 % |
| Transversion |
T>G |
All |
238889 |
0.96 % |
| Transversion |
G>T |
All |
534363 |
2.16 % |
| Transversion |
A>T |
All |
414147 |
1.67 % |
| Transversion |
T>A |
All |
411905 |
1.66 % |
| Transversion |
C>G |
All |
200837 |
0.81 % |
| Transversion |
G>C |
All |
195280 |
0.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
479831 |
17.89 % |
| Transition |
G>A |
Passed |
458426 |
17.09 % |
| Transition |
T>C |
Passed |
480005 |
17.90 % |
| Transition |
C>T |
Passed |
459250 |
17.12 % |
| Transversion |
A>C |
Passed |
106752 |
3.98 % |
| Transversion |
C>A |
Passed |
101091 |
3.77 % |
| Transversion |
T>G |
Passed |
106215 |
3.96 % |
| Transversion |
G>T |
Passed |
101291 |
3.78 % |
| Transversion |
A>T |
Passed |
76428 |
2.85 % |
| Transversion |
T>A |
Passed |
76386 |
2.85 % |
| Transversion |
C>G |
Passed |
117785 |
4.39 % |
| Transversion |
G>C |
Passed |
118358 |
4.41 % |
| |
|
|
|
|
| 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 |
7.98 |
22022370 |
2760773 |
| Passed |
2.33 |
1877512 |
804306 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |