/EXTERNAL BLUEPRINT/variants/K012036_K012064_K012065_K012066_K012067_K012068_K012069_K012070_K012071_K012112_K012113_11_lane_gembs
BACK
SAMPLE K012036_K012064_K012065_K012066_K012067_K012068_K012069_K012070_K012071_K012112_K012113_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
835756763 |
4052504 |
0.48 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
835756763 |
100% |
821830960 |
98.33 % |
13925803 |
1.67 % |
| |
|
|
|
|
|
|
| Passed |
11343939 |
1.36 % |
3641920 |
0.44 % |
7702019 |
67.90 % |
| Filtered |
824412824 |
98.64 % |
818189040 |
99.56 % |
6223784 |
54.86 % |
| |
|
|
|
|
|
|
| q20 |
644848336 |
78.22 % |
640516197 |
78.28 % |
4332139 |
69.61 % |
| q20,qd2 |
105880636 |
12.84 % |
104801164 |
12.81 % |
1079472 |
17.34 % |
| q20,mq40 |
54248277 |
6.58 % |
53932460 |
6.59 % |
315817 |
5.07 % |
| q20,qd2,mq40 |
18912848 |
2.29 % |
18839496 |
2.30 % |
73352 |
1.18 % |
| mq40 |
516794 |
0.06 % |
94281 |
0.01 % |
422513 |
6.79 % |
| qd2 |
4820 |
0.00 % |
4606 |
0.00 % |
214 |
0.00 % |
| qd2,mq40 |
1083 |
0.00 % |
836 |
0.00 % |
247 |
0.00 % |
| qd2,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| fs60,mq40 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
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 |
4074384 |
22.00 % |
| Transition |
G>A |
All |
1471818 |
7.95 % |
| Transition |
T>C |
All |
5121928 |
27.66 % |
| Transition |
C>T |
All |
721863 |
3.90 % |
| Transversion |
A>C |
All |
656093 |
3.54 % |
| Transversion |
C>A |
All |
1219340 |
6.58 % |
| Transversion |
T>G |
All |
751916 |
4.06 % |
| Transversion |
G>T |
All |
1091434 |
5.89 % |
| Transversion |
A>T |
All |
871686 |
4.71 % |
| Transversion |
T>A |
All |
1208142 |
6.52 % |
| Transversion |
C>G |
All |
612139 |
3.31 % |
| Transversion |
G>C |
All |
718004 |
3.88 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
69481 |
17.03 % |
| Transition |
G>A |
Passed |
52359 |
12.83 % |
| Transition |
T>C |
Passed |
104389 |
25.58 % |
| Transition |
C>T |
Passed |
24125 |
5.91 % |
| Transversion |
A>C |
Passed |
17169 |
4.21 % |
| Transversion |
C>A |
Passed |
24759 |
6.07 % |
| Transversion |
T>G |
Passed |
18783 |
4.60 % |
| Transversion |
G>T |
Passed |
16644 |
4.08 % |
| Transversion |
A>T |
Passed |
10045 |
2.46 % |
| Transversion |
T>A |
Passed |
23255 |
5.70 % |
| Transversion |
C>G |
Passed |
20645 |
5.06 % |
| Transversion |
G>C |
Passed |
26432 |
6.48 % |
| |
|
|
|
|
| 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 |
1.60 |
11389993 |
7128754 |
| Passed |
1.59 |
250354 |
157732 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |