/EXTERNAL BLUEPRINT/variants/K006327_15_lane_gembs
BACK
SAMPLE K006327_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1080013175 |
567009710 |
52.50 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1080013175 |
100% |
1061590200 |
98.29 % |
18422975 |
1.71 % |
| |
|
|
|
|
|
|
| Passed |
568570430 |
52.64 % |
565896249 |
53.31 % |
2674181 |
0.47 % |
| Filtered |
511442745 |
47.36 % |
495693951 |
46.69 % |
15748794 |
2.77 % |
| |
|
|
|
|
|
|
| q20 |
419063503 |
81.94 % |
417468354 |
84.22 % |
1595149 |
10.13 % |
| q20,qd2 |
62753713 |
12.27 % |
49147949 |
9.91 % |
13605764 |
86.39 % |
| q20,mq40 |
15297274 |
2.99 % |
15198871 |
3.07 % |
98403 |
0.62 % |
| mq40 |
7185704 |
1.40 % |
7032508 |
1.42 % |
153196 |
0.97 % |
| qd2 |
3617090 |
0.71 % |
3525773 |
0.71 % |
91317 |
0.58 % |
| q20,qd2,mq40 |
3419253 |
0.67 % |
3237352 |
0.65 % |
181901 |
1.16 % |
| qd2,mq40 |
95514 |
0.02 % |
83144 |
0.02 % |
12370 |
0.08 % |
| q20,qd2,fs60 |
3304 |
0.00 % |
0 |
0.00 % |
3304 |
0.02 % |
| fs60 |
2237 |
0.00 % |
0 |
0.00 % |
2237 |
0.01 % |
| qd2,fs60 |
2091 |
0.00 % |
0 |
0.00 % |
2091 |
0.01 % |
| qd2,fs60,mq40 |
1693 |
0.00 % |
0 |
0.00 % |
1693 |
0.01 % |
| q20,qd2,fs60,mq40 |
766 |
0.00 % |
0 |
0.00 % |
766 |
0.00 % |
| fs60,mq40 |
600 |
0.00 % |
0 |
0.00 % |
600 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
2952404 |
10.70 % |
| Transition |
G>A |
All |
9806193 |
35.54 % |
| Transition |
T>C |
All |
2735386 |
9.91 % |
| Transition |
C>T |
All |
9552321 |
34.62 % |
| Transversion |
A>C |
All |
200435 |
0.73 % |
| Transversion |
C>A |
All |
490164 |
1.78 % |
| Transversion |
T>G |
All |
218132 |
0.79 % |
| Transversion |
G>T |
All |
478586 |
1.73 % |
| Transversion |
A>T |
All |
394706 |
1.43 % |
| Transversion |
T>A |
All |
398398 |
1.44 % |
| Transversion |
C>G |
All |
186405 |
0.68 % |
| Transversion |
G>C |
All |
176249 |
0.64 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
330532 |
19.64 % |
| Transition |
G>A |
Passed |
286041 |
17.00 % |
| Transition |
T>C |
Passed |
330179 |
19.62 % |
| Transition |
C>T |
Passed |
285129 |
16.94 % |
| Transversion |
A>C |
Passed |
60804 |
3.61 % |
| Transversion |
C>A |
Passed |
53316 |
3.17 % |
| Transversion |
T>G |
Passed |
60039 |
3.57 % |
| Transversion |
G>T |
Passed |
53459 |
3.18 % |
| Transversion |
A>T |
Passed |
35322 |
2.10 % |
| Transversion |
T>A |
Passed |
34728 |
2.06 % |
| Transversion |
C>G |
Passed |
76236 |
4.53 % |
| Transversion |
G>C |
Passed |
77133 |
4.58 % |
| |
|
|
|
|
| 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 |
9.85 |
25046304 |
2543075 |
| Passed |
2.73 |
1231881 |
451037 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |