Table 2. Assembly statistics and BLAST results against nr for the G. bimaculatus de novo transcriptome assembly.
Parameter1 | Value |
# bp Raw reads | 1,483,726,666 |
Maximum raw read length | 803 |
Minimum raw read length | 13 |
Median raw read length | 364 |
Maximum assembled read length | 771 |
Minimum assembled read length | 20 |
Median assembled read length | 358 |
# Isogroups2 (“genes”) | 16,456 |
Mean # isotigs per isogroup | 1.2 |
# Isotigs | 21,512 |
Maximum isotig length | 10,865 |
Minimum isotig length | 57 |
Median isotig length | 1,054.5 |
# Isotigs with BLAST hit against nr 3, E-value cutoff e-10 (% of all isotigs) | 11,135 (51.8%) |
# Isotigs with BLAST hit against nr, E-value cutoff e-5 (% of all isotigs) | 11,943 (55.5%) |
Mean # contigs per isotig | 1.7 |
# Singletons | 120,805 |
Maximum singleton length | 620 |
Minimum singleton length | 50 |
Median singleton length | 250.5 |
# Singletons with BLAST hit against nr, E-value cutoff e-10 (% of all singletons) | 7,914 (6.6%) |
# Singletons with BLAST hit against nr, E-value cutoff e-5 (% of all singletons) | 10,815 (9.0%) |
# Non-redundant assembly products (NRAP) | 142,317 |
# NRAP with BLAST hit against nr, E-value cutoff e-10 (% of all NRAP) | 19,049 (13.4%) |
# NRAP with BLAST hit against nr, E-value cutoff e-5 (% of all NRAP) | 22,758 (16.0%) |
Total # BLAST hits4 (nr) | 22,758 |
Average coverage/bp | 51.3 |
Values for number of raw reads, number and % of raw reads assembled (passed quality filters described in main text), number of contigs, isotig N50, % of singletons, total number of assembly products, and number of unique BLAST hits against nr, are shown in Table 1.
Because isogroups are collections of isotigs that are hypothesized to originate from the same gene, they do not comprise a single sequence and so cannot be mapped to nr using BLAST.
nr = NCBI non-redundant database.
For BLAST against nr the E-value cutoff was 1e-5. For breakdown of BLAST hits among different classes of assembly sequences, see Table 3.