Schema for SEDEF Segmental Dups - SEDEF Segmental Duplications
  Database: hub_567047_hs1    Primary Table: hub_567047_sedefSegDups Data last updated: 2022-07-16
Big Bed File Download: /gbdb/hs1/sedefSegDups/sedefSegDups.bb
Item Count: 83,516
The data is stored in the binary BigBed format.

Format description: SedDups Features Description
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart166093136Alignment start
chromEnd166094637Alignment end
namechr3:188232930-188234430Position of the matching duplication
score0fake score
strand++ or - for strand
thickStart166093136thick start
thickEnd166094637thick end
color199,199,199Color reflects %id. Approximatly matches WGAC track.
chrom2chr3Reference sequence chromosome or scaffold
Start2188232930second alignment start
End2188234430second alignment end
score29.0Score
strand2-+ or - for strand
maxlen1501max_len
alnlen1507aln_len
indela6indel_a
indelb7indel_b
alnB1494alnB
matchB1371matchB
mismatchB123mismatchB
transitionsB82transitionsB
transvertionsB41transvertionsB
fracMatch0.917671fracMatch
fracMatchIndel0.909754fracMatchIndel
jck0.0872086jck
k2K0.0879077k2K
alngaps5aln_gaps
uppercaseA1446uppercaseA
uppercaseB1421uppercaseB
uppercaseMatches1307uppercaseMatches
alnMatches1371aln_matches
alnMismatches123aln_mismatches
alnGapBases13aln_gap_bases
filterScore0.91461filter_score
satBases0sat bases
uniqueID11877unique_id
originalTrueWhether the SD is the original SD, or the symetric copy.
telo0is telomeric
peri0is pericentromeric
acro0is acrocentric
telo20other is telomeric
peri20other is pericentromeric
acro20other is acrocentric

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndcolorchrom2Start2End2score2strand2maxlenalnlenindelaindelbalnBmatchBmismatchBtransitionsBtransvertionsBfracMatchfracMatchIndeljckk2KalngapsuppercaseAuppercaseBuppercaseMatchesalnMatchesalnMismatchesalnGapBasesfilterScoresatBasesuniqueIDoriginalteloperiacrotelo2peri2acro2
chr1166093136166094637chr3:188232930-1882344300+166093136166094637199,199,199chr31882329301882344309.0-15011507671494137112382410.9176710.9097540.08720860.087907751446142113071371123130.91461011877True000000
chr1166093146166094605chr1:171039515-1710409750+166093146166094605191,191,191chr11710395151710409758.1-14601464541455134610976330.9250860.9193990.07892490.07965144614061302134610990.921918011878True000000
chr1166093163166094594chr14:15947933-159493600+166093163166094594217,217,217chr14159479331594936010.7+143114365914221283139110290.902250.8934540.1047340.10666171431139712561283139140.897831011879True000010
chr1166093164166094595chr9:7473481-74749100+166093164166094595206,206,206chr9747348174749109.7-14311437681423129812592330.9121570.9032710.09342740.094601851431142912981298125140.908964011880True000000
chr1167139299167140754chr7:65942102-659435260+167139299167140754167,167,167chr765942102659435267.5-14551455031142413467846320.9452250.9250860.05687860.057049110132312941227134678310.938633011892True000010
chr1167374451167379183chr15:27007303-270121130+167374451167379183175,175,175chr1527007303270121139.8-481048681365846744389285194910.9390240.9016020.06359740.06399023725002510226143892851940.931649011895True000000
chr1167406808167407963chr19:23994786-239959390+167406808167407963204,204,0chr1923994786239959391.4+115511550211531139141040.9878580.9861470.01224160.0122581211361144112211391420.986147011898True000010
chr1167406812167407958chr2:206597439-2065984620+167406812167407958177,177,177chr220659743920659846217.9+114611561013310139496445190.9368210.8209340.06599930.066479661131980914949641430.931305011899True000000
chr1167406825167407961chr7:65790103-657912470+167406825167407961189,189,189chr7657901036579124710.2-114411582214112210408254280.9269160.89810.07689430.07740579113411161013104082360.91954011901True000010
chr1167406833167407901chr5:142421549-1424226170+167406833167407901142,142,142chr51424215491424226174.0+1068107244106410293515200.9671050.9598880.03363790.03364641068102699010293580.963483011902True000000

SEDEF Segmental Dups (hub_567047_sedefSegDups) Track Description
 

Description

A track showing segmental duplications as generated by sedef on the assembly: T2T-CHM13-v2.0 Column descriptions can be found here: columns.

Display Conventions and Configuration

This section describes track configuration controls, or any special display conventions such as the meaning of different colors in your tracks.

The colours used for level of similary segmentation standard:

less than 90% similarityPurple
90 - 98% similarityLight to dark gray
98 - 99% similarityYellow
greater than 99% similarityOrange

Methods

Sedef was run with default parameters on a RepeatMasked genome assembly. The resulting output (final.bed) was then converted into a browser friendly format (bed9 + extra fields).

Credits

References

M. R. Vollger et al., Segmental duplications and their variation in a complete human genome. Science. 2022 April 1; eabj6965. DOI: 10.1126/science.abj6965

Numanagic I, Gökkaya AS, Zhang L, Berger B, Alkan C, Hach F. Fast characterization of segmental duplications in genome assemblies. Bioinformatics. 2018 Sep 1;34(17):i706-i714. PMID: 30423092; PMC: PMC6129265