How IGV recognize the reference region?

[dkrtndhkd]

I aligned my target NGS data to chr7, not whole genome seqeunce,

when I view the result bam file by IGV,

how IGV can recognize the bam file is aligned to chr7?

the reference info is also included in the bam file?

As you might see before, the gene names which are in chr7 are also seen.

there's no gene name info in the bam file.

Curiooooooooooous!!!

[arvid]

IGV comes with the annotation (e.g. gene locations) of some typically used genomes. When you aligned to a chr7 reference, "chr7" was stored in the BAM file. When you loaded it into IGV, IGV detected that "chr7" information and loaded the annotation for that chromosome onto the gene track...

[dkrtndhkd]

Thankyou