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 analyzes the traces from the sequencing machines and assigns a quality score to these. These quality scores are used by the Phrap assembly program, which gives quality scores for the bases on the assembly as well.

chr_alt chromosomes

What is chr_alt?

The chr_alt chromosomes, such as chr5_KI270794v1_alt, 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 Alt Haplotypes track if one is available.

Additional information on alternative loci can be found on our hg38 patches blog post as well as the Genome Reference Consortium (GRC) website.

chr_fix chromosomes

What is chr_fix?