dd63f1db2fabe42eed12f9311b482f3c8fee4b94 kuhn Sun Sep 26 13:20:43 2021 -0700 fixed single-char typo diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html index 75d3994..819bcbf 100755 --- src/hg/htdocs/FAQ/FAQdownloads.html +++ src/hg/htdocs/FAQ/FAQdownloads.html @@ -414,31 +414,31 @@ target="_blank">Phred</a> analyzes the traces from the sequencing machines and assigns a quality score to these. These quality scores are used by the <a href="http://www.phrap.org/" target="_blank">Phrap</a> assembly program, which gives quality scores for the bases on the assembly as well.</p> <a name="downloadAlt"></a> <h2>chr_alt chromosomes</h2> <h6>What is chr_alt?</h6> <p> The chr_alt chromosomes, such as <em>chr5_KI270794v1_alt</em>, are alternative sequences that differ from the reference genome currently available for a few assemblies including danRer11, mm10, hg19, and hg38. These are regions of the genome that exhibit sufficient variability to prevent adequate representation by a single sequence. UCSC labels these haplotype sequences by appending "_alt" to their names. These alternative loci scaffolds (such as KI270794.1 in the hg38 assembly, referenced as chr5_KI270794v1_alt in the browser), are mapped to the genome and provide -suppemental genomic information on these variable locations. To find the regions these alternate +supplemental genomic information on these variable locations. To find the regions these alternate sequences correspond to in the genome you may use the <a href="../cgi-bin/hgTrackUi?db=hg38&g=altSeqLiftOverPsl" target="_blank">Alt Haplotypes track</a> if one is available. </p> <p> Additional information on alternative loci can be found on our <a href="http://genome.ucsc.edu/blog/patches/" target="_blank">hg38 patches blog post</a> as well as the <a href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml#ALTERNATE" target="_blank">Genome Reference Consortium (GRC) website</a>. </p> <a name="downloadFix"></a> <h2>chr_fix chromosomes</h2> <h6>What is chr_fix?</h6>