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)

表S1 修剪前后的RNA读段数量及Bowtie2与Hisat2的比对成功率
表S2 基于AbYSS对DNA测序未比对读段进行从头组装的统计汇总
表S3 结合所有组织样本，基于Trinity对RNA测序未比对读段进行从头组装的统计汇总
表S4 DNA未比对读段的从头组装重叠群与NT数据库的显著比对结果汇总。其中，序列一致性（Identity）为完全匹配碱基的百分比；查询覆盖度（query coverage）为每个比对主体对应的查询序列覆盖度
表S5 RNA未比对读段的开放阅读框（Open Reading Frame, ORF）与NR数据库的显著比对结果汇总。其中，序列一致性（Identity）为完全匹配碱基的百分比；错配数（mismatch）为错配碱基的总数量
表S6 RNA未比对读段的从头组装重叠群与NT数据库的显著比对结果汇总。其中，序列一致性（Identity）为完全匹配碱基的百分比；查询覆盖度（query coverage）为每个比对主体对应的查询序列覆盖度；MAPQ为使用GMAP将序列比对回P. major基因组时得到的比对质量值
表S7 RNA数据集各组织类型的读段计数
表S8 RNA数据集中新发现的基因列表
表S9 基于AbYSS对亚硫酸氢盐测序未比对读段进行从头组装的统计汇总
表S10 亚硫酸氢盐处理后的未比对读段的从头组装重叠群与NT数据库的显著比对结果汇总。其中，序列一致性（Identity）为完全匹配碱基的百分比；查询覆盖度（query coverage）为每个比对主体对应的查询序列覆盖度
表S11 新组装的P. major线粒体的注释信息。其中，Score为非编码RNA（non-coding RNA, ncRNA）的e值以及蛋白编码基因预测的质量值
表S12 新组装的P. major线粒体与P. major基因组NT数据库的显著比对结果汇总。其中，序列一致性（Identity）为完全匹配碱基的百分比
（XLSX格式，大小21932 kb）