Possibly missing good minor calls in Iso

[Phelimb]

Tim found several minor calls which were pheno R.

Based off the plots here: https://cycloid.well.ox.ac.uk:9999/ipython/notebooks/phelim/archive/Proportion%20of%20mixed%20calls%20in%20tb.ipynb we don't catch any ISO minor which are TP.

    +---------------------------------------------------------------------------------------------------------------------+
    |          comid      variant   pheno   ref   mutation    A1   C1   G1   T1   A2    C2   G2   T2   A3    C3   G3   T3 |
    |---------------------------------------------------------------------------------------------------------------------|

1. | IF00133966-S10 katG_S315T R AGC ANC 27 0 0 0 0 12 19 0 0 33 0 0 |
2. | 9549-01 katG_S315T R AGC ANC 39 0 0 0 0 36 4 0 0 40 0 0 |
3. | TRL0025711-S14 katG_S315T R AGC ANC 41 0 0 0 1 33 7 0 0 41 0 0 |
4. | 8648-04 katG_S315T R AGC ANC 19 0 0 0 0 16 3 0 0 20 0 0 |

5. C00014853 katG_S315T R AGC ANC 111 0 0 0 1 58 53 0 0 107 0 0

6. | C00008743 katG_S315T R AGC ANC 129 0 0 0 0 37 90 0 0 129 0 0 |
7. | C00008814 katG_S315T R AGC ANC 238 0 0 0 0 162 92 0 0 251 0 4 | +---------------------------------------------------------------------------------------------------------------------+

[Phelimb]

We call all of these samples as R with the exception of one which we call as r.

            },
            "lineage": {
            "European/American": "Major"
            }
    },
    "susceptibility" :{
            "Isoniazid": "R",
            "Rifampicin": "Inconclusive",
            "Ethambutol": "S",
            "Pyrazinamide": "S",
            "Quinolones": "S",
            "Streptomycin": "S",
            "Amikacin": "S",

            "katG_S315X" :{
                    "R_per_cov": "100",
                    "S_per_cov": "100",
                    "R_median_cov": "12",
                    "S_median_cov": "13",
                    "conf": "1",
            "induced_resistance": "Isoniazid"
            }
    }

} { "expected_depth": "32",

"phylogenetics": {

            },
            "lineage": {
            "Beijing/East Asia": "Major"
            }
    },
    "susceptibility" :{
            "Isoniazid": "R",
            "Rifampicin": "R",
            "Ethambutol": "R",
            "Pyrazinamide": "S",
            "Quinolones": "S",
            "Streptomycin": "R",
            "Amikacin": "S",

            "katG_S315X" :{
                    "R_per_cov": "100",
                    "S_per_cov": "100",
                    "R_median_cov": "35",
                    "S_median_cov": "5",
                    "conf": "80",
            "induced_resistance": "Isoniazid"
            },
            "embB_M306X" :{
                    "R_per_cov": "100",
                    "S_per_cov": "100",
                    "R_median_cov": "32",
                    "S_median_cov": "5",
                    --
            },
            "lineage": {
            "European/American": "Major"
            }
    },
    "susceptibility" :{
            "Isoniazid": "R",
            "Rifampicin": "R",
            "Ethambutol": "S",
            "Pyrazinamide": "S",
            "Quinolones": "S",
            "Streptomycin": "R",
            "Amikacin": "S",

            "katG_S315X" :{
                    "R_per_cov": "100",
                    "S_per_cov": "100",
                    "R_median_cov": "25",
                    "S_median_cov": "4",
                    "conf": "56",
            "induced_resistance": "Isoniazid"
            },
            "rpsL_K43R" :{
                    "R_per_cov": "100",
                    "S_per_cov": "100",
                    "R_median_cov": "32",
                    "S_median_cov": "2",

            },
            "lineage": {
            "Beijing/East Asia": "Major"
            }
    },
    "susceptibility" :{
            "Isoniazid": "R",
            "Rifampicin": "R",
            "Ethambutol": "R",
            "Pyrazinamide": "S",
            "Quinolones": "S",
            "Streptomycin": "R",
            "Amikacin": "S",

            "katG_S315X" :{
                    "R_per_cov": "100",
                    "S_per_cov": "100",
                    "R_median_cov": "15",
                    "S_median_cov": "2",
                    "conf": "35",
            "induced_resistance": "Isoniazid"
            },
            "embB_M306X" :{
                    "R_per_cov": "100",
                    "S_per_cov": "0",
                    "R_median_cov": "21",
                    "S_median_cov": "0",

cat: _Net_banyan_data2_users_phelimb_tb_fastqs_C00008814*/stdout: No such file or directory }, "lineage": { "East Africa / Indian ocean": "Major" } }, "susceptibility" :{ "Isoniazid": "R", "Rifampicin": "S", "Ethambutol": "S", "Pyrazinamide": "S", "Quinolones": "S", "Streptomycin": "S",

"Amikacin": "S",

            "katG_S315X" :{
                    "R_per_cov": "100",
                    "S_per_cov": "100",
                    "R_median_cov": "46",
                    "S_median_cov": "46",
                    "conf": "14",
            "induced_resistance": "Isoniazid"
            }
    }

} { "expected_depth": "86",

"phylogenetics": {

            },
            "lineage": {
            "East Africa / Indian ocean": "Major"
            }
    },
    "susceptibility" :{
            "Isoniazid": "r",
            "Rifampicin": "S",
            "Ethambutol": "S",
            "Pyrazinamide": "S",
            "Quinolones": "S",
            "Streptomycin": "r",
            "Amikacin": "S",

            "katG_S315X" :{
                    "R_per_cov": "100",
                    "S_per_cov": "100",
                    "R_median_cov": "31",
                    "S_median_cov": "78",
                    "conf": "99",
            "induced_resistance": "Isoniazid"
            },
            "rpsL_K43R" :{
                    "R_per_cov": "100",
                    "S_per_cov": "100",
                    "R_median_cov": "33",
                    "S_median_cov": "87",                        

[Phelimb]

@iqbal-lab these look good to me. Can we close this?

[iqbal-lab]

Yes :-)

[iqbal-lab]

Although there is a question as to why that one r is not on the ipython plot - only matters for the paper figure

[Phelimb]

Yeah, I'll reopen until I check this. Could be different commits.

[iqbal-lab]

In fact, the R allele has more coverage for

IF00133966-S10 (19 versus 12) C00008743 (90 versus 37)

and basically the same coverage for

C00014853 (53 versus 58)

It still high coverage for

C00008814 (92 versus 162)

and it has low coverage for the remaining 3 (<10 reads).

So arguably we should call 2 of these major, and maybe the one where we have as much covg, and for the rest is minor. We've called it Major for all of them. Good data to revisit one day when we care about better estimation of frequency, but at that point I won't do it on the basis of coverage at a single SNP