Genome sequence report

Genome assembly sequence accessions, chromosome, and length

Genome sequence report

Genome assembly sequence accessions, chromosome, and length

The downloaded genome package contains a genome sequence data report in JSON Lines format in the file:

ncbi_dataset/data/<assembly>/sequence_report.jsonl

Each line of the genome assembly sequence data report file is a JSON object that represents a single genome assembly sequence record. The schema of the genome assembly sequence record is defined in the table below where each row in SequenceInfo describes a single field in the report.

Table fields that include a Table Field Mnemonic can be used with the dataformat command-line tool's --fields option. Refer to the dataformat CLI tool reference to see how you can use this tool to transform assembly sequence data reports from JSON Lines to tabular formats.

Sample report

{
  "assemblyAccession": "GCF_000001405.40",
  "assemblyUnit": "Primary Assembly",
  "assignedMoleculeLocationType": "Chromosome",
  "chrName": "1",
  "gcCount": "103674491",
  "gcPercent": 41.5,
  "genbankAccession": "CM000663.2",
  "length": 248956422,
  "refseqAccession": "NC_000001.11",
  "role": "assembled-molecule",
  "sequenceName": "1",
  "ucscStyleName": "chr1",
  "unlocalizedCount": 9
}

SequenceInfo Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`assemblyAccession`	`accession`	Assembly Accession	`string`	The GenColl assembly accession	`GCF_000001405.40`
`chrName`	`chr-name`	Chromosome name	`string`	The name of the associated chromosome. The name “Un” indicates that the chromosome is unknown.	`21` `MT` `Un`
`ucscStyleName`	`ucsc-style-name`	UCSC style name	`string`	Name ascribed to this sequence by the UC Santa Cruz genome browser	`chr21` `chrM` `Un`
`sortOrder`	`ordering`	Ordering	`uint32`	A sort order value assigned to the sequence	`1` `25`
`assignedMoleculeLocationType`	`mol-type`	Molecule type	`string`	The type of molecule represented by the sequence	`Chromosome` `Mitochondrion`
`refseqAccession`	`refseq-seq-acc`	RefSeq seq accession	`string`	The RefSeq accession of the sequence	`NC_000021.9`
`assemblyUnit`	`assm-unit-acc`	Assembly-unit accession	`string`	The NCBI Assembly accession of the associated assembly unit. Assembly units can include the primary assembly and non-nuclear assembly units	`GCF_000001305.15`
`length`	`seq-length`	Seq length	`uint32`	The length of the sequence in nucleotides	`46709983`
`genbankAccession`	`genbank-seq-acc`	GenBank seq accession	`string`	The GenBank accession of the sequence	`CM000683.2`
`gcPercent`	`gc-percent`	GC Percent	`float`	The percentage of GC base-pairs in the chromosome
`unlocalizedCount`	`unlocalized-count`	Unlocalized Count	`uint32`	Number of scaffolds that are unlocalized on a given chromosome
`assemblyUnplacedCount`	`assembly-unplaced-count`	Assembly Unplaced Count	`uint32`	Number of unplaced scaffolds for a given assembly accession
`role`	`role`	Role	`string`
`sequenceName`	`sequence-name`	Sequence name	`string`	The sequence name

Scalar Value Types

Protocol buffers type	Notes	C++	Python	Java	Go
`double`		`double`	`float`	`double`	`float64`
`float`		`float`	`float`	`float`	`float32`
`int32`	Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint32 instead.	`int32`	`int`	`int`	`int32`
`int64`	Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint64 instead.	`int64`	`int/long`	`long`	`int64`
`uint32`	Uses variable-length encoding.	`uint32`	`int/long`	`int`	`uint32`
`uint64`	Uses variable-length encoding.	`uint64`	`int/long`	`long`	`uint64`
`sint32`	Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int32s.	`int32`	`int`	`int`	`int32`
`sint64`	Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int64s.	`int64`	`int/long`	`long`	`int64`
`fixed32`	Always four bytes. More efficient than uint32 if values are often greater than 2^28.	`uint32`	`int`	`int`	`uint32`
`fixed64`	Always eight bytes. More efficient than uint64 if values are often greater than 2^56.	`uint64`	`int/long`	`long`	`uint64`
`sfixed32`	Always four bytes.	`int32`	`int`	`int`	`int32`
`sfixed64`	Always eight bytes.	`int64`	`int/long`	`long`	`int64`
`bool`		`bool`	`boolean`	`boolean`	`bool`
`string`	A string must always contain UTF-8 encoded or 7-bit ASCII text.	`string`	`str/unicode`	`String`	`string`
`bytes`	May contain any arbitrary sequence of bytes.	`string`	`str`	`ByteString`	`[]byte`

Generated May 21, 2024