del

[Phelimb]

At 6 hours, it starts to call everything R, which needs fixing. Basically, I think it says with v low covg, you expect low covg, and we're ok with a fraction of a gene..etc - so it's calling this

    "called_genes" :{
            "aacAaphD" :{
                    "per_cov": "56",
                    "median_cov": "1",
                    "conf": "637",
            "induced_resistance": "Gentamicin"
            },
            "blaZ" :{
                    "per_cov": "49",
                    "median_cov": "0",
                    "conf": "656",
            "induced_resistance": "Penicillin"
            },
            "dfrA" :{
                    "per_cov": "41",
                    "median_cov": "0",
                    "conf": "129",
            "induced_resistance": "Trimethoprim"
            },
            "ermA" :{
                    "per_cov": "14",
                    "median_cov": "0",
                    "conf": "61",
            "induced_resistance": "Erythromycin"
            },
            "fusB" :{
                    "per_cov": "21",
                    "median_cov": "0",
                    "conf": "83",
            "induced_resistance": "FusidicAcid"
            },
            "vga_A_LC" :{
                    "per_cov": "16",
                    "median_cov": "0",
                    "conf": "176",
            "induced_resistance": "Clindamycin"
            },
            "mecA" :{
                    "per_cov": "85",
                    "median_cov": "2",
                    "conf": "4670",
            "induced_resistance": "Methicillin"
            },
            "tetK" :{
                    "per_cov": "15",
                    "median_cov": "0",
                    "conf": "141",
            "induced_resistance": "Tetracycline"
            },
            "vanA" :{
                    "per_cov": "7",
                    "median_cov": "0",
                    "conf": "39",
            "induced_resistance": "Vancomycin"
            },
            "mupA" :{
                    "per_cov": "16",
                    "median_cov": "0",
                    "conf": "373",
            "induced_resistance": "Mupirocin"
            }

[iqbal-lab]

To be clear, this is the ONTbranch

[iqbal-lab]

.

[Phelimb]

You can create them here https://github.com/iqbal-lab/Mykrobe-predictor/labels