/EXTERNAL BLUEPRINT/variants/K006267_7_lane_gembs
BACK
SAMPLE K006267_7_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1134547080 |
781025391 |
68.84 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1134547080 |
100% |
1114545877 |
98.24 % |
20001203 |
1.76 % |
| |
|
|
|
|
|
|
| Passed |
782333689 |
68.96 % |
779428318 |
69.93 % |
2905371 |
0.37 % |
| Filtered |
352213391 |
31.04 % |
335117559 |
30.07 % |
17095832 |
2.19 % |
| |
|
|
|
|
|
|
| q20 |
260725495 |
74.02 % |
259012328 |
77.29 % |
1713167 |
10.02 % |
| q20,qd2 |
40020673 |
11.36 % |
25410104 |
7.58 % |
14610569 |
85.46 % |
| qd2 |
23748344 |
6.74 % |
23580596 |
7.04 % |
167748 |
0.98 % |
| q20,mq40 |
13390307 |
3.80 % |
13272417 |
3.96 % |
117890 |
0.69 % |
| mq40 |
11224482 |
3.19 % |
11015433 |
3.29 % |
209049 |
1.22 % |
| q20,qd2,mq40 |
2924560 |
0.83 % |
2684679 |
0.80 % |
239881 |
1.40 % |
| qd2,mq40 |
160090 |
0.05 % |
142002 |
0.04 % |
18088 |
0.11 % |
| q20,qd2,fs60 |
7516 |
0.00 % |
0 |
0.00 % |
7516 |
0.04 % |
| fs60 |
3670 |
0.00 % |
0 |
0.00 % |
3670 |
0.02 % |
| qd2,fs60 |
3528 |
0.00 % |
0 |
0.00 % |
3528 |
0.02 % |
| qd2,fs60,mq40 |
2552 |
0.00 % |
0 |
0.00 % |
2552 |
0.01 % |
| q20,qd2,fs60,mq40 |
1115 |
0.00 % |
0 |
0.00 % |
1115 |
0.01 % |
| fs60,mq40 |
1043 |
0.00 % |
0 |
0.00 % |
1043 |
0.01 % |
| q20,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
2953491 |
7.24 % |
| Transition |
G>A |
All |
16395166 |
40.18 % |
| Transition |
T>C |
All |
2816028 |
6.90 % |
| Transition |
C>T |
All |
16294780 |
39.93 % |
| Transversion |
A>C |
All |
197233 |
0.48 % |
| Transversion |
C>A |
All |
433733 |
1.06 % |
| Transversion |
T>G |
All |
208956 |
0.51 % |
| Transversion |
G>T |
All |
427404 |
1.05 % |
| Transversion |
A>T |
All |
359222 |
0.88 % |
| Transversion |
T>A |
All |
352668 |
0.86 % |
| Transversion |
C>G |
All |
189090 |
0.46 % |
| Transversion |
G>C |
All |
180992 |
0.44 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
455072 |
18.70 % |
| Transition |
G>A |
Passed |
414523 |
17.03 % |
| Transition |
T>C |
Passed |
454103 |
18.66 % |
| Transition |
C>T |
Passed |
414915 |
17.05 % |
| Transversion |
A>C |
Passed |
91806 |
3.77 % |
| Transversion |
C>A |
Passed |
86411 |
3.55 % |
| Transversion |
T>G |
Passed |
91681 |
3.77 % |
| Transversion |
G>T |
Passed |
85818 |
3.53 % |
| Transversion |
A>T |
Passed |
64265 |
2.64 % |
| Transversion |
T>A |
Passed |
64262 |
2.64 % |
| Transversion |
C>G |
Passed |
105334 |
4.33 % |
| Transversion |
G>C |
Passed |
105850 |
4.35 % |
| |
|
|
|
|
| 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 |
16.37 |
38459465 |
2349298 |
| Passed |
2.50 |
1738613 |
695427 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |