dbSNP Map Information
Chromosome Reports below are synced with the current NCBI
genome assembly.
NCBI now integrates dbSNP entries with other
sequence and mapping resources via
BLAST
and E-PCR
analysis. This analysis associates all SNPs with a nucleotide sequence record
and/or sequence
contig.
RefSNPs
that have been mapped to a contig will be annotated as a 'variation'
feature on the appropriate contig. This variation annotation will include a
/db_xref
qualifier (i.e. database pointer) back to dbSNP. If the SNP is in a gene
region, it is now annotated on the appropriate
NCBI Reference
Sequence mRNA record. If the variation is inferred to change the protein
peptide sequence (a non-synonymous substitution), it is annotated as a
variation feature on the protein sequence as well.
Currently 1,420,877, (79 %) of human refSNPs have been mapped onto the current
human genome sequence assembly. dbSNP submissions for other species are
currently being mapped into GenBank accession coordinates. The figure to the
left shows the distribution of one measure of mapping quality: the number of
distinct positions in the genome where we have found a high quality hit based
on sequence similarity. The vast majority of the submitted human data (74%) has
been mapped uniquely to the current genome assembly.
When submissions in repetitive elements are
excluded from analysis, 89.6% of the set of currently mapped refSNPs hit
exactly one place in the genome, 5.4% hit twice, and 4.9% hit between 3 and 10
times. Less than 0.1% of the database hits more than 10 places. The two columns
to the right reveal 1,493 refSNPs that hit indiscriminately across the genome,
but were not completely masked by RepeatMasker. As a group, these refSNPs seem
to reside in repeat motifs such as an Aluor LINE , and the
submissions did not include sufficient unique flanking sequence to contstrain
the placement of a particular refSNP to a single position in the genome.
RefSNPs that hit more than twice to the genome will not be annotated on genome
sequence. RefSNPs that hit twice are annotated with a warning of ambiguous map
location.
The distribution of mapped
refSNPs by chromosome is shown above. Histogram bars indicate the number of
refSNPs mapped to each chromosome. The triangles show the mean inter-marker
distance between refSNPs computed as chromosome length (in kb) divided by
marker density. Chromosome Y is off the scale (right) with a mean inter-marker
density of 15.8 kb. Intermarker density cannot be computed for markers on
unplaced contigs (chromosome Un). Marker density is not uniform across
chromosomes. The figures are provided for intra-chromosomal comparisons only.
Refer to the NCBI MapViewer Variation Map (below) to examine marker density in
regions of interest.
Chromosome Maps:
The table below provides statistics for the
refSNPs mapped to the
human
genome.
Chromosome
Report for
ordered list
of refSNPs: |
Map
View |
RefSNPs on chromosome: |
Chromosome
Length (Mb): |
Mean
Intermarker
Distance (Kb) |
| 1
|
 |
142,629 |
252.5 |
1.77 |
| 2
|
|
114,530 |
238.0 |
2.08 |
| 3
|
|
100,670 |
204.4 |
2.03 |
| 4
|
|
86,173 |
189.6 |
2.20 |
| 5
|
|
117,256 |
180.5 |
1.54 |
| 6
|
|
106,080 |
178.0 |
1.68 |
| 7
|
|
85,708 |
160.4 |
1.87 |
| 8
|
|
60,246 |
143.4 |
2.38 |
| 9
|
|
64,928 |
131.7 |
2.03 |
| 10
|
|
67,505 |
139.7 |
2.07 |
| 11
|
|
92,726 |
141.2 |
1.52 |
| 12
|
|
67,263 |
138.4 |
2.06 |
| 13
|
|
61,001 |
116.7 |
1.91 |
| 14
|
|
50,904 |
105.4 |
2.07 |
| 15
|
|
44,587 |
98.9 |
2.22 |
| 16
|
|
47,532 |
92.6 |
1.95 |
| 17
|
|
40,743 |
83.3 |
2.05 |
| 18
|
|
54,813 |
81.3 |
1.48 |
| 19
|
|
32,039 |
77.1 |
2.41 |
| 20
|
|
33,693 |
61.8 |
1.84 |
| 21
|
|
26,284 |
46.2 |
1.76 |
| 22
|
|
31,765 |
47.2 |
1.49 |
| X
|
|
35,933 |
150.3 |
4.18 |
| Y
|
|
3,723 |
59 |
15.85 |
|
