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.
Car_ign_all_nucleotide_contigs_from_Ray_assembly
FASTA 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 ignobilis
Car_ign_only_1200bp+_nucleotide_contigs_from_Ray_assembly
FASTA file of only nucleotide contigs >=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
Car_mel_all_nucleotide_contigs_from_Ray_assembly
FASTA 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 melampygus
Car_mel_only_1200bp+_nucleotide_contigs_from_Ray_assembly
FASTA file of only nucleotide contigs >=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
Car_ign_all_100+amino_acids_ORFs_from_1200bp+_contigs
FASTA file of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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
Car_ign_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio.parsed
Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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.filtered
Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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. >=80.
Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_hits
Gene list of all hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_unique_hits
Gene list of only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_vs_unique_hits.diff
Difference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_as_aa
FASTA file of open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_ign_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu.parsed
Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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.filtered
Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_hits
Gene list of all hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_unique_hits
Gene list of only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_vs_unique_hits.diff
Difference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_as_aa
FASTA file of open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_mel_all_100+amino_acids_ORFs_from_1200bp+_contigs
FASTA file of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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
Car_mel_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio.parsed
Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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.filtered
Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_hits
Gene list of all hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_unique_hits
Gene list of only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_vs_unique_hits.diff
Difference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_as_aa
FASTA file of open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_mel_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu.parsed
Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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.filtered
Parsed BLAST output of all potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_hits
Gene list of all hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_unique_hits
Gene list of only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_vs_unique_hits.diff
Difference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_as_aa
FASTA file of open reading frames (ORFs) >=100 amino acids extracted from nucleotide contigs >=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 >=80.
Car_ign_all_intragenomic_SNP_indel_variation_from_1200bp+_contigs
Variant call format (VCF) file containing potential single nucleotide polymorphisms (SNPs) and indels variation extracted from nucleotide contigs >=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.filtered
Variant call format (VCF) file containing potential single nucleotide polymorphisms (SNPs) and indels variation extracted from nucleotide contigs >=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+_contigs
Variant call format (VCF) file containing potential single nucleotide polymorphisms (SNPs) and indels variation extracted from nucleotide contigs >=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.filtered
Variant call format (VCF) file containing potential single nucleotide polymorphisms (SNPs) and indels variation extracted from nucleotide contigs >=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.
