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Table 1 Summary statistics of sequencing reads, assembly, and annotations

From: Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae)

Category Valuex
Primary
de novo Assembly
Redundancy Reduced
Assembly
Collapsed Iso-Seq Set
Raw reads   670,892,713 1,463,943
Total length of raw reads (Mbp)   206,368 288
Quality filtered & trimmed reads 615,064,938 1,270,618
Total length of prepared reads (Mbp) 80,819 146
Total Contigs 156,724 105,307 65,696
 Read utilization (%) 95 78 87
 Avg. length of contigs 941 1058 2227
 Contig size N50 1265 1494 3581
 Min. contig length 300 300 80
 Max. contig length 21,363 21,363 9831
 Total nucleotides in assembly 147,537,886 111,466,222 146,320,100
Annotation Statistics
 InterProScan 156,723 (99%) 105,307 (100%) 48,482 (74%)
 BLASTx (nr) hits 85,974 (55%) 45,192 (43%) 59,553 (91%)
 Uniquely aligning to genomey 99,110 (63%) 95,274 (90%) 63,042 (96%)
 Functionally annotatedz 66,810 (43%) 33,782 (32%) 51,536 (78%)
  1. xColumns represent the three assemblies utilized in the differential gene expression analysis. The primary de novo assembly comprised of next-generation sequence reads assembled using a k-mer size of 41 and a bubble size of 350 in the Qiagen CLC Genomics Workbench 11.0. The redundancy-reduced assembly was developed via reference mapping to multiple members in the Andropogonae and further reduced by cluster enrichment with CD-Hit. The collapsed iso-seq set was developed from pooled RNA samples of the same experimental tissue and collapsed with the Cupcake TOFU pipeline
  2. yTranscripts mapped, with GMAP, to a single genomic locus of a preliminary reference assembly with 95% coverage and identity
  3. zUnigenes annotated with one or more gene ontology terms