TB-Profiler result

Run: SRR22528526

Summary

Run ID: SRR22528526

Sample name:

Date: 04-04-2023 04:17:58

Number of reads: 2084108

Percentage reads mapped: 99.58

Strain: lineage4.1.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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
gyrB 6734 p.Asn499Asp missense_variant 0.53 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.29 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.46 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.45 kanamycin, capreomycin, aminoglycosides, amikacin
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
gyrB 6052 p.Ile271Met missense_variant 1.0
gyrA 6487 c.-815C>G upstream_gene_variant 1.0
gyrB 7221 p.Ser661Thr missense_variant 1.0
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 576100 p.Asp251Glu missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416699 p.Leu217Val missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673579 p.Arg47Pro missense_variant 0.15
fabG1 1673608 p.Gly57Cys missense_variant 0.14
inhA 1673865 c.-337C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154832 p.Leu427Pro missense_variant 1.0
katG 2156255 c.-144T>G upstream_gene_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726142 c.-51G>A upstream_gene_variant 1.0
pepQ 2860113 c.306C>G synonymous_variant 0.11
pepQ 2860128 p.Phe97Leu missense_variant 0.13
pepQ 2860131 c.288C>G synonymous_variant 0.15
pepQ 2860140 c.279A>G synonymous_variant 0.14
pepQ 2860144 p.Val92Gly missense_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.2
whiB7 3568428 c.252A>G synonymous_variant 0.24
whiB7 3568437 c.243T>C synonymous_variant 0.14
whiB7 3568441 p.Lys80Thr missense_variant 0.13
rpoA 3878597 c.-90G>C upstream_gene_variant 0.13
rpoA 3878608 c.-101C>G upstream_gene_variant 0.12
clpC1 4040874 c.-170C>G upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.2
embB 4247055 p.Leu181Gln missense_variant 0.24
embB 4247080 p.Phe189Leu missense_variant 0.16
embB 4247112 p.Leu200Arg missense_variant 0.12
embB 4248319 c.1806A>T synonymous_variant 0.21
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0