TB-Profiler result

Run: ERR688041
Summary

Run ID: ERR688041

Sample name:

Date: 02-04-2023 03:52:30

Number of reads: 23408071

Percentage reads mapped: 99.57

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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 7581 p.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289081 p.Pro54Leu missense_variant 1.0 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.97 kanamycin, amikacin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327069 c.404_405insAT frameshift_variant 0.96 ethionamide
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
mshA 576400 c.1053C>T synonymous_variant 1.0
rpoB 761461 p.Arg552Leu missense_variant 1.0
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
PPE35 2169320 p.Leu431Phe missense_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.22
ald 3087367 p.Ala183Val missense_variant 1.0
rpoA 3877536 c.972C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.12
ubiA 4269124 p.Ala237Val missense_variant 1.0
whiB6 4338307 p.Ala72Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0