Additional file 1: of Exploring the unmapped DNA and RNA reads in a songbird genome

Table S1. Number of RNA reads before and after trimming and mapping success of Bowtie2 and Hisat2. Table S2. Summary statistics from the de novo assembly of unmapped reads from DNA sequencing using AbYSS. Table S3. Summary statistics from the de novo assembly of unmapped reads from RNA sequencing using Trinity and all tissues combined. Table S4. Summary of the significant alignments of de novo assembled contigs from DNA unmapped reads to the nt -database. Identity is the percentage of identical matches; query coverage is the query coverage per subject. Table S5. Summary of the significant alignments of ORFs from RNA unmapped reads to the nr -database. Identity is the percentage of identical matches; mismatch is number of mismatches. Table S6. Summary of the significant alignments of de novo assembled contigs from RNA unmapped reads to the nt -database. Identity is the percentage of identical matches; query coverage is the query coverage per subject; MAPQ is the mapping quality value from the mapping back to the P. major genome with GMAP. Table S7. Read count per tissue type of the RNA dataset. Table S8. List of newly discovered genes in the RNA dataset. Table S9. Summary statistics from the de novo assembly of unmapped reads from bisulfite sequencing using ABySS. Table S10. Summary of the significant alignments of de novo assembled contigs from bisulfite treated unmapped reads to the nt -database. Identity is the percentage of identical matches; query coverage is the query coverage per subject. Table S11. Annotation of the newly assembled P. major mitochondria. Score is the e-values for ncRNA and quality values for protein coding gene predictions. Table S12. Summary of the significant alignments of the newly assembled P.major mitochondria to the P.major genome nt -database. Identity is the percentage of identical matches. (XLSX 21932 kb)