+This track shows mobile element insertions (MEIs) identified by +MELT +on the SweGen +cohort of 1,000 Swedish whole-genome samples (Ameur et al. 2017). Each +site is an insertion of an Alu, L1 (LINE-1), SVA or HERV-K mobile +element relative to the reference. The SweGen short-variant frequency +data for the same cohort is shown in the +SweGen variant frequencies subtrack of +the Variant Frequencies collection. +
+ +| Class | MEIs |
|---|---|
| Alu | 14,467 |
| L1 | 2,429 |
| SVA | 1,131 |
| HERVK | 73 |
| Total (GRCh37) | 18,100 |
| Total (after liftOver to hg38) | 18,090 |
+For each MEI, the track reports the mobile element class, the +insertion length, the MELT subfamily call (e.g. AluYa5, L1Ta), the +target-site duplication sequence, the MELT ASSESS quality score, +nearby gene context if the insertion lies in or close to a gene, the +allele count (MELT_AN; despite the name this is the number of allele +observations, not the allele number), the alt-allele frequency, and +the MELT FILTER status. +
+ ++An insertion has zero length on the reference: it attaches between +two adjacent reference bases without replacing any of them. Following +the convention used by MELT and by the other MEI tracks in this +collection, each MEI is drawn as a 1-bp block sitting on the anchor +base — the reference base immediately to the left of the +insertion attachment point. The inserted mobile element itself is not +present in the reference and is therefore not drawn. The item label is +class-altAlleleCount. +
+ ++Items are colored by element class: +
++The score column encodes the alt-allele frequency on a 0-1000 scale. +Filters allow restricting items by element class, insertion length, +allele frequency, MELT ASSESS quality score (0-5) and the MELT FILTER +status. The track keeps both PASS and non-PASS sites; non-PASS sites +carry one of the MELT site-level filter codes: +
++The SweGen project sequenced 1,000 Swedish individuals on Illumina +HiSeq X with 150 bp paired-end reads (Covaris E220 fragmentation, ~350 +bp insert), and aligned the reads to the GRCh37 reference with +BWA-MEM v0.7.12. Mobile element insertions were called by +MELT +v2.0.2 (Gardner et al. 2017) in MELT-Split mode using the default +ALU, HERVK, LINE1 and SVA mobile-element zip packages, on all 1,000 +samples. Per-site allele counts and frequencies (MELT_AN and MELT_AF +in INFO) were computed across the cohort; the VCF does not contain +per-sample genotype columns. The analysis used the Perl SMELT +pipeline (github.com/J35P312/SMELT) on the UPPMAX Bianca +cluster in early 2018, by Diana Ekman, Jesper Eisfeldt and Daniel +Nilsson. +
+ ++The site-level VCF +MELT_SWEGEN.20180314.ALU_HERVK_LINE1_SVA.vcf was obtained +from the SweGen download portal +(swefreq.nbis.se/dataset/SweGen/download, access +requires a brief approval). The VCF uses GRCh37 contigs without a +"chr" prefix; the conversion adds the prefix, drops the VCF +header, maps SVTYPE codes (ALU, LINE1, SVA, +HERVK) to the element class names used here, copies INFO +fields through to the BED, and writes a bed9+9 file with 1-bp anchor +intervals. The hg19 BED was then lifted to hg38 with UCSC +liftOver (-tab -bedPlus=9), which mapped 18,090 of +18,100 records; 10 records fell into hg38-deleted regions and were +dropped. The lifted BED was sorted and converted to bigBed using the +meiSwegen.as schema. Conversion and lift steps are +documented in the +makeDoc file; the scripts live in +src/hg/makeDb/scripts/mei. +
+ ++The SweGen download portal also distributes a hg38 variant set +(SweGen38_{ALU,L1,SVA,HERV}.vcf) for the same 1,001 samples, +produced with SVDB after re-running on GRCh38. We chose to lift the +original GRCh37 MELT VCF instead because the hg38 SVDB files +contain 138,853 records (about 7.7× the MELT site count), and +roughly 60% of those records are singletons (OCC=1) without +any quality filter. They also drop most of the per-site annotation: +no MELT subfamily call (e.g. AluYa5, L1Ta), no insertion length +(SVLEN=0 everywhere), no target-site duplication, no MELT +ASSESS quality score, no gene context and no FILTER stratification +(every site is marked PASS). The GRCh37 MELT VCF, lifted to +hg38, gives a much more informative and quality-filtered set, at the +cost of 10 records that fell into hg38-deleted regions. +
+ ++Due to SweGen license restrictions, the underlying VCF and the bigBed +derived from it cannot be redistributed from the UCSC Genome Browser. +The Table Browser and download server are disabled for this track. To +obtain the source data, follow the request procedure at the +SweGen +download portal. +
+ ++Thanks to Adam Ameur, Diana Ekman, Jesper Eisfeldt, Daniel Nilsson +and the SweGen consortium for generating and releasing the MELT MEI +callset, and to SciLifeLab for producing the underlying SweGen WGS +data. +
+ ++Ameur A, Dahlberg J, Olason P, Vezzi F, Karlsson R, Martin M, Viklund J, Kähäri AK, Lundin P, Che H +et al. + +SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish +population. +Eur J Hum Genet. 2017 Nov;25(11):1253-1260. +PMID: 28832569; PMC: PMC5765326 +
+ ++Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, Mills RE, 1000 Genomes Project +Consortium, Devine SE. + +The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology. +Genome Res. 2017 Nov;27(11):1916-1929. +PMID: 28855259; PMC: PMC5668948 +
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