TB-Profiler result

Run: ERR4800677

Summary

Run ID: ERR4800677

Sample name:

Date: 01-04-2023 09:59:18

Number of reads: 2635778

Percentage reads mapped: 99.55

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.95
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.96
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 6734 p.Asn499Asp missense_variant 0.94 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asp missense_variant 0.92 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.67 isoniazid
katG 2141614 c.-13506_*12274del transcript_ablation 1.0 isoniazid
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 0.98
gyrA 8040 p.Gly247Ser missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.15
rpoB 762889 p.His1028Arg missense_variant 0.97
rpoC 764995 c.1626C>G synonymous_variant 0.98
rpoC 766939 p.Asn1190Lys missense_variant 0.27
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
rrl 1475707 n.2050T>C non_coding_transcript_exon_variant 0.96
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.97
thyA 3073868 p.Thr202Ala missense_variant 0.95
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
clpC1 4038287 c.2418C>T synonymous_variant 0.97
embC 4242182 p.Ala774Ser missense_variant 0.94
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244283 p.Pro351Thr missense_variant 0.98
embB 4246529 p.Ser6Arg missense_variant 0.27
embB 4246584 p.Arg24Pro missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.94