The taxon id was classified as 1

[ala98412]

Hello,

I'm currently working with kraken2 using a dataset downloaded from NCBI (ERR4082713). I've noticed that there's a read classified as taxid 1 in both the fastq_1 and fastq_2 files.

The classified reads looks like this:

_fastq1: @ERR4082713.144642 144642 length=251 kraken:taxid|1 CATTTCATCTGTGAGCAAAGGTGGCATATCAGTAAGGCCGGTTTACTTTTGTGCACAAATGAGGTCTCTAGCGTCAATATGACCAAGGCAATCAACATATTGTTTGAAGAAGGAAGCATCTGGAAGTGTCACTTTGTTGAAACGTAGATAGGCAATAAATGACAGATTGTTTGGTTCTGAGGGATCTGGTGATATTTGTGAAAAGTTAAAACTACCAAGATCTTTACTTGGTCGTGTGTTGTAAATCTGTT + DDDDDFFFFBBBBBBBB44BGFGBBB4455DDDGHG44BA2A22ADFGHHHHHHHHHHHHHBABBBDDFHHH0B1BADD55DD@GHHGHHHH333BBFHH4BBDB?33D33B113B?BDB343333B3?DDDDD3DDBG443B?BBB?3?3222B@2DDDDD@222DDF2>?????1??11/?>0>>>>>0>=HGHHG1<====/<=00==G0=<<<<.<<CCFHH0=<<<:0<<<C.<<.<<<<<0<<<F

_fastq2: @ERR4082713.144642 144642 length=251 kraken:taxid|1 GTGGTGTTTCAACTGAATGTAGCAATCTTTTGTTGCGATGGGGTCTTATTTGTACACAACTAAACCGTGCTTTATCTGGAATAGCTGTTGTCAAAGACATAAACAGCCAAGAAGTTTTTGCACAAGGCAAACAACTTTACAGAACACCACAAATTAAAGATGTTGGGGGTTTTAACTTTTCACAAATATCACCAGATCCATCTCAAAAAAGTAAGAGGTCATTTATTGAAGATCTTCTTTTCAACATTGTG + AAAABB4>BBBBBB44BBG5B6DDDBBD5DDFFHHH2AB2ABB2BBG5ADFGD5D5ABBBBBB3BBEEHGGDD5DAD5BBBGHBG5BDB3B54B43BCGBBBBBB2B?BF11F3BBBB?/BBB320/?BBBBB/?3BF4BF2BBBBB//?/?@2F2@@@@@2@@2///<->>>=<1><<DD0=0<<===00=<0<<D/;<:0;00000;-.0;;9;0.99;CFGGGGFGFBCF0;90=;BFG0;;C/;0=9

This seems odd to me because I couldn't find taxid 1 on NCBI. Moreover, I performed a BLAST search on this read on NCBI, and the result indicated that it is a SARS-CoV-2 sequence, aligning with the result of other reads in same dataset.

How can I resolve this unusual result?

Best, Jui-Hung

[jenniferlu717]

taxid 1 is the root of the taxonomy tree. Essentially your reads matched equally on either side of the taxonomy tree so a more specific classification cannot be made