Cephalotaxus_harringtonia-20120822
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stats.txt:  Summary  statistics  associated  with contigs.fa. In-
cludes the total number of sequences and bases in the contig set,
N50,  etc.   Q1,  Q2, Q3 are the quartiles of the reported contig
lengths. B1000 and B2000 indicate the  percentage  of  bases  in-
volved in contigs at least 1000 bp and 2000 bp, respectively.

--
contigs.fa:  Contigs  from the assembly, minimum 100 bp. Possibly
includes UTRs. Sequences contain IUPAC ambiguity codes represent-
ing    ambiguous   bases,   http://www.bioinformatics.org/sms/iu-
pac.html.

--
cds.fa: Coding regions associated with contigs, as  predicted  by
ESTscan, minimum 100 bp.  Sequence identifiers for these predict-
ed CDS are provided suffixes _1, _2, etc., to accommodate  multi-
ple  predictions, and to indicate association with predicted pro-
tein products. Sequences contain IUPAC ambiguity codes represent-
ing    ambiguous   bases,   http://www.bioinformatics.org/sms/iu-
pac.html. Note that the total number of predicted  CDS  might  be
higher  or  lower  than the number of contigs. This can be due to
the reporting threshold of 100 nt  or  multiple  predictions  per
contig.

--
peptides.fa:  Protein  products  associated with contigs, as pre-
dicted by ESTScan, minimum 30 aa.  Sequence identifiers for these
predicted  products  correspond  to the associated nucleotide se-
quence in contig.fa, and are provided suffixes _1, _2,  etc.,  to
accommodate  multiple  predictions. Note that the total number of
predicted peptides might be higher or lower than  the  number  of
contigs.  This  can be due to the reporting threshold of 30 aa or
multiple predictions per contig.

--
readcounts/contigs/all_alignments.dat: Read  counts  obtained  by
post  hoc  alignment  of reads using BWA to reported contigs with
default parameters. Tab-delimited columns with the format

  id all_aligned all_aligned_fraction unique_aligned paired_aligned len

where id is the contig identifier, for example, Cephalotaxus_har-
ringtonia-20120822|1234;  all_aligned  is  the  number  of  reads
aligned   to   this   contig,   including   multimapped    reads.
all_aligned_fraction  is the number of reads aligned to this con-
tig, but in the case of multimapped reads, the read  is  assigned
fractionally  to the hit contigs. This has the advantage that the
sum of the all_aligned_fraction counts equals the total number of
reads  that  aligned.  unique_aligned is the number of reads that
aligned uniquely to this contig; and paired_aligned is the number
of  read  pairs aligned to this contig.  len is the length of the
contig in bp.

                        * * * NOTE * * *
While this information is sufficient to compute common normalized
values such as RPKM (reads per kilobase of transcript per million
mapped reads) and FPKM (fragments per kilobase of transcript  per
million mapped reads), these read counts are provided for quality
assessment of the contig set only.  For  differential  expression
analyses, it is recommended more sophisticated estimators of rel-
ative expression level be employed. See for example:  Salzman  J,
Jiang H, Wong WH. Statistical modeling of RNA-Seq data. Statisti-
cal Science 26 (2011).

--
annot/pfam.gff3, ...: Models matching predicted protein  products
(peptides.fa)  reported  in GFF3 format; based on HMMER3 searches
against the Pfam-A, Superfamily, and TIGRFAMs model  sets.  These
are  restricted  to  full-sequence-evalue  <= 1.0e-5 with the top
five hits reported.

Association with InterPro terms is indicated in the Ontology_term
attribute, and is based on the assertions (InterPro -> model, In-
terPro -> protein accession) made by InterPro. Currently InterPro
associations from Superfamily hits are not computed.

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National Center for Genome Resources
http://www.ncgr.org