Additional file 5: of Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken

Figure S1. Aligned reads showing the insertion site of Hf_ERV on chicken chromosome 10. Aligned reads are shown in gray; multicolored “rainbow” reads are soft-clipped. Left clip and right clip sequences match the 5′ and 3′ of the LTR sequence, respectively. Discordant reads are in cyan which are well aligned in this figure (Chr10), while their mate pairs are aligned to Chr1, either to LOC770705 or LOC107052718, both retrovirus related genes, because there is no retrovirus sequence at this target site on chromosome 10 in the reference genome. Altogether, this alignment suggests a retrovirus insertion located between the left and right clips, which contains the 6 bp target site duplication (TSD) sequence. Reads are obtained from BioSample Accession SAMEA104432213 (Pool of Silver Sebright Bantam) and aligned to GalGal6. (DOCX 214 kb)