Mouse strain pangenome (minigraph on GRCm39), indexed for JBrowse 2 =================================================================== These files are a graph built here from published assemblies, plus tabix-indexed BED projections of it, so that JBrowse can query a locus without downloading the graph. Unlike the bovine set beside it, no pangenome graph was published for these assemblies -- this one was constructed. See "How it was built". Assemblies ---------- 19 sequence sets: UCSC mm39 (GRCm39) as the reference backbone, plus 18 inbred and wild-derived strain assemblies, all fetched from UCSC hgdownload. The strain assemblies are the Mouse Genomes Project / Ensembl mouse strain assemblies as rehosted in UCSC GenArk. mm39 GRCm39 (C57BL/6J reference) goldenPath/mm39 C57BL_6J_T2T GCA_964188535.1 CAST_EiJ_T2T GCA_964188545.1 C57BL_6NJ GCA_921999865.2 NZO_HlLtJ GCA_947593165.1 BALB_cJ GCA_921997145.2 FVB_NJ GCA_921998635.2 129S1_SvImJ GCA_921998555.2 C3H_HeJ GCA_921997125.2 AKR_J GCA_922000895.2 DBA_2J GCA_921998315.2 A_J GCA_921998355.2 LP_J GCA_947599735.1 NOD_ShiLtJ GCA_921998325.2 CBA_J GCA_921998905.2 CAST_EiJ GCA_921999005.2 WSB_EiJ GCA_921998345.2 JF1_MsJ GCA_921999095.2 PWK_PhJ GCA_921998335.2 Each assembly's contigs were mapped to mm39 chromosome names through the chromAlias table UCSC publishes beside it, and one sequence per chromosome was extracted and renamed to PanSN: mm39#0#chrN for the reference, #1#chrN for a strain. Reference --------- UCSC mm39 == GRCm39. https://jbrowse.org/ucsc/mm39/config.json How it was built ---------------- Per chromosome, in reference-first order: minigraph -cxggs -t 8 mm39.chrN.fa .chrN.fa ... minigraph emits rGFA natively, so SN/SO/SR tags are read from the graph rather than reconstructed -- this is the difference from the bovine set, whose published graphs are plain GFA with P lines and whose tags had to be recovered by walking paths. The 21 per-chromosome graphs were then renumbered onto one segment-id space (chromosome k's ids shifted by k * 10,000,000, which is well clear of the 1,321,274 segments the whole graph holds) and concatenated into a single rGFA. Two audits ran on the result and both are clean: every S line's SN tag matches mm39#0#chr* or #1#chr*, and no segment id repeats. gfatools stat on the assembled graph: segments 1,321,274 links 1,867,122 arcs 3,734,244 max rank 18 total segment length 3,138,127,925 bp rank-0 (mm39) length 2,723,414,844 bp max degree 13 average degree 1.413 The rank-0 total is GRCm39's own length, which is the check that the reference thread is intact. Compute: 27.4 h of minigraph wall time over the 21 chromosomes, run two at a time. chrX was the longest at 3 h 50 m, chr14 at 2 h 19 m and chr7 at 2 h 14 m; chr19 was the shortest at 22 m. Coverage, and the two sex chromosomes ------------------------------------- Every autosome (chr1-chr19) carries all 19 assemblies. chrX carries 18. C57BL_6J_T2T contributes no X: its chromAlias table names 238 sequences and none of them is an X or a Y, so there was nothing to extract. It was not dropped for quality. chrY carries ONE -- mm39 alone. No strain assembly in this set has a Y sequence. The chrY entry is therefore a bare reference thread, not a graph: one segment, zero links, 91 MB of GRCm39 chrY sequence. It is kept so the graph covers the whole reference, but nothing varies along it and it is deliberately not offered as a whole-chromosome view in JBrowse. Files ----- mouse-mm39-minigraph.rgfa.gz the graph itself (bgzipped rGFA) mouse-mm39-minigraph.segs.bed.gz rGFA segments, one row per node mouse-mm39-minigraph.links.bed.gz rGFA links, one row per edge (+ .tbi; these two are one track -- JBrowse's RgfaTabixAdapter is given the shared prefix `mouse-mm39-minigraph` and appends both suffixes itself) mouse-mm39-minigraph.tier10000.segs.bed.gz level-of-detail tier: one node mouse-mm39-minigraph.tier10000.links.bed.gz per top-level bubble, so a whole (+ .tbi) chromosome draws in a few hundred nodes instead of tens of thousands mouse-mm39-minigraph.bubbles.bed.gz gfatools bubble output (+ .tbi), read both as a feature track and as the segments-per-bubble curve mouse-mm39-minigraph.alleles.bed.gz allele inventory (+ .tbi): one row per allele the graph holds, stated against the reference span it replaces, carrying a CIGAR so an insertion draws at its real size Licence and attribution ----------------------- The underlying assemblies are the Mouse Genomes Project strain assemblies, distributed by ENA/NCBI and rehosted by UCSC GenArk; mm39 is GRCm39 from GRC. Cite the assemblies, not this file. The graph and the projections here are derived work produced for the JBrowse 2 demos and carry no additional restriction. Built 2026-09-02 with minigraph 0.21-r606 (-cxggs) and gfatools 0.5-r296-dirty.