TB-Profiler result

Run: ERR4553863
Summary

Run ID: ERR4553863

Sample name:

Date: 01-04-2023 06:23:22

Number of reads: 972842

Percentage reads mapped: 99.54

Strain: lineage4

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
gyrA 7582 p.Asp94Gly missense_variant 0.75 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.95 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.96 isoniazid
katG 2155289 p.Thr275Ala missense_variant 0.79 isoniazid
pncA 2288928 p.Gly105Asp missense_variant 0.86 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.29
rpoB 759939 p.Pro45Ser missense_variant 0.78
rpoC 765150 p.Gly594Glu missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155617 c.495T>C synonymous_variant 0.82
PPE35 2168975 c.1638C>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065080 p.His371Arg missense_variant 0.12
thyA 3074220 c.252A>T synonymous_variant 0.79
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>A synonymous_variant 0.29
fbiA 3641447 p.Thr302Met missense_variant 0.97
rpoA 3877553 p.Glu319Lys missense_variant 0.94
clpC1 4040410 p.Gly99Cys missense_variant 0.16
clpC1 4040605 p.Leu34Ile missense_variant 0.31
embC 4240897 c.1035C>G synonymous_variant 0.94
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.43
embB 4249408 c.2895G>A synonymous_variant 0.5
ubiA 4269308 p.Phe176Leu missense_variant 0.85
ethR 4327303 c.-246G>A upstream_gene_variant 0.79
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408011 c.192G>C synonymous_variant 0.87