TB-Profiler result

Run: ERR2653151
Summary

Run ID: ERR2653151

Sample name:

Date: 31-03-2023 22:35:53

Number of reads: 7230815

Percentage reads mapped: 97.6

Strain: lineage4.3.3

Drug-resistance: HR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.99
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
gyrB 6620 p.Asp461Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288903 c.329_338delACGAGAACGG frameshift_variant 0.98 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.99 kanamycin, amikacin
ethA 4326419 c.1054delG frameshift_variant 0.99 ethionamide, 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8257 p.Lys319Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761032 p.Gln409Arg missense_variant 1.0
rpoB 761105 c.1301_1309delTGGACCAGA disruptive_inframe_deletion 0.99
rpoC 764995 c.1626C>G synonymous_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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3065641 c.548_550delCCG disruptive_inframe_deletion 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087715 c.897dupG frameshift_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840463 p.Arg320Trp missense_variant 0.58
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245201 p.Thr657Pro missense_variant 1.0
whiB6 4338296 p.Trp76Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407914 p.Arg97Cys missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0