| Format Acronym | Format Name | File Extension | Encoding | Notes |
|---|---|---|---|---|
| FASTA | .fa .fasta | Text | First Used by the FASTA software. | |
| FASTQ | .fq .fastq | Text | Adds sequence quality values to FASTA. | |
| GenBank | .gb .gbk | Text | Developed by NCBI for GenBank Project. | |
| SAM | Sequence Alignment Map | .sam | Text | |
| BAM | Binary Alignment Map | .bam | Binary | Same information as SAM but in binary format. |
| BAI | Binary Alignme/Map Index File | .bai | Binaru | A table of contents for a BAM file. |
| VCF | Variant Call Format | .vcf | Text | Information about variations from a reference. |
| GTF | Gene Transfer Format | .gtf | Text | Old but still popular. |
| GFF | General Feature Format | .gff | Text | An enhancement to GTF. |
| GFF3 | General Feature Format Version 3 | .gff3 | Text | An enhancement to GFF. |