I am aiming to determine the species/subspecies identity of a (possibly bacteria) sample. I applied the following [sendsketch][1] command:

    sendsketch.sh in=contigs.fasta,

where the input file (contigs.fasta) was previously generated from the raw paired-end read file using SPAdes. The results of the above command can be viewed here: [here][2]. The sendsketch website states that WKID is "the column that tells you the actual sequence similarity (disregarding size)." As a result, I believe I should focus on H. macacae since it had the highest WKID value (along with KID = 0.05%; ANI = 96.6%; Contam = 2.5%).

1) Are the output values here sound or a cause for alarm? Is the WKID (38.9%) or KID (0.05%) value too low? Or are other values questionable? 

2) If the values are sound, I hope to check the mapping rate (using BWA) of the sample to the H. macacae genome (so that I can use it as a reference genome for further steps). However, I am a bit stuck on figuring out the appropriate sequence to download. The taxID number output from the sendsketch was 398626. It seems there are 46 sequences available on NCBI ([here][3]). How should I go about determining the optimal H. macacae sequence to map my samples to? 

Side note: I have a similar problem with H. mastomyrinus, the second-highest WKID value from sendsketch. There are 17 sequences available on NCBI [here][4]. In this case, some are 16S and some are 23S. How do I know which sequence to map against in this scenario?

  [1]: http://seqanswers.com/forums/showthread.php?t=74019
  [2]: https://ibb.co/HpT4nJP
  [3]: https://www.ncbi.nlm.nih.gov/nuccore/?term=txid398626%5BOrganism%5D
  [4]: https://www.ncbi.nlm.nih.gov/nucleotide?term=txid287948[Organism]
There's only one H. macacae genome in my slightly dated local RefSeq Bacteria copy:

    GCF_000507845.1	PRJNA224116	SAMN00690723	AZJI00000000.1	representative genome	1357400	398626	Helicobacter macacae MIT 99-5501	strain=MIT 99-5501		latest	Scaffold	Major	Full	2013/12/13	Heli_maca_MIT_99-5501_V1	Broad Institute	GCA_000507845.1	identical	ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/507/845/GCF_000507845.1_Heli_maca_MIT_99-5501_V1		assembly from type material

