DOI: 10.5061/dryad.6gr7t
title: Data from: "Complete mitochondrial and partial nuclear genomes for the jack species Caranx ignobilis (Forsskål, 1775) and C. melampygus (Cuvier, 1833) (Perciformes:Carangidae) from the High Hawaiian Islands" in Genomic Resources Notes accepted 1 October 2013 – 30 November 2013

description: Complete mitochondrial and partial nuclear genomes for the jack species
 Caranx ignobilis (Forsskål, 1775) and C. melampygus (Cuvier, 1833)
 (Perciformes:Carangidae) from the High Hawaiian Islands are presented
 along with annotation and characterization of intragenomic single
 nucleotide polymorphism (SNPs) and indel variation.
description: Car_ign_all_nucleotide_contigs_from_Ray_assemblyFASTA file of all nucleotide contigs assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilisCar_ign_only_1200bp+_nucleotide_contigs_from_Ray_assemblyFASTA file of only nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilisCar_mel_all_nucleotide_contigs_from_Ray_assemblyFASTA file of all nucleotide contigs assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygusCar_mel_only_1200bp+_nucleotide_contigs_from_Ray_assemblyFASTA file of only nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygusCar_ign_all_100+amino_acids_ORFs_from_1200bp+_contigsFASTA file of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilisCar_ign_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio.parsedParsed BLAST output of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI.Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio.parsed.filteredParsed BLAST output of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores. &gt;=80.Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_hitsGene list of all hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_unique_hitsGene list of only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_vs_unique_hits.diffDifference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_as_aaFASTA file of open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_ign_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu.parsedParsed BLAST output of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI.Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu.parsed.filteredParsed BLAST output of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_hitsGene list of all hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_unique_hitsGene list of only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_vs_unique_hits.diffDifference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_as_aaFASTA file of open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_mel_all_100+amino_acids_ORFs_from_1200bp+_contigsFASTA file of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygusCar_mel_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio.parsedParsed BLAST output of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI.Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio.parsed.filteredParsed BLAST output of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_hitsGene list of all hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_unique_hitsGene list of only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_vs_unique_hits.diffDifference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_as_aaFASTA file of open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_mel_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu.parsedParsed BLAST output of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI.Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu.parsed.filteredParsed BLAST output of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_hitsGene list of all hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_unique_hitsGene list of only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_vs_unique_hits.diffDifference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_as_aaFASTA file of open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.Car_ign_all_intragenomic_SNP_indel_variation_from_1200bp+_contigsVariant call format (VCF) file containing potential single nucleotide polymorphisms (SNPs) and indels variation extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. The following filters were applied with the program vcf-annotate: –f +/c3,10/Q=20/d=15/D=25. This file contains SNPs and indels that DID and DID NOT pass filtering.Car_ign_intragenomic_SNP_indel_variation_from_1200bp+_contigs.filteredVariant call format (VCF) file containing potential single nucleotide polymorphisms (SNPs) and indels variation extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. The following filters were applied with the program vcf-annotate: –f +/c3,10/Q=20/d=15/D=25. This file contains ONLY SNPs and indels that DID pass filtering.Car_mel_all_intragenomic_SNP_indel_variation_from_1200bp+_contigsVariant call format (VCF) file containing potential single nucleotide polymorphisms (SNPs) and indels variation extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. The following filters were applied with the program vcf-annotate: –f +/c3,10/Q=20/d=15/D=25. This file contain SNPs and indels that DID and DID NOT pass filtering.Car_mel_intragenomic_SNP_indel_variation_from_1200bp+_contigs.filteredVariant call format (VCF) file containing potential single nucleotide polymorphisms (SNPs) and indels variation extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. The following filters were applied with the program vcf-annotate: –f +/c3,10/Q=20/d=15/D=25. This file contains ONLY SNPs and indels that DID pass filtering.