TB-Profiler result

Run: SRR7592356

Summary

Run ID: SRR7592356

Sample name:

Date: 04-04-2023 19:49:52

Number of reads: 2890497

Percentage reads mapped: 99.57

Strain: lineage4.7

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
lineage4.7 Euro-American (mainly T) T1;T5 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.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
tlyA 1918205 c.269dupG frameshift_variant 0.32 capreomycin
tlyA 1918551 c.613dupG frameshift_variant 0.14 capreomycin
tlyA 1918667 c.731_732dupGC frameshift_variant 0.39 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715347 c.-15C>G upstream_gene_variant 1.0 kanamycin
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4327416 c.56_57dupCG frameshift_variant 0.91 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 575811 p.Tyr155Ser missense_variant 1.0
mshA 576479 p.Pro378Ala missense_variant 0.18
rpoC 765084 p.Arg572His 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
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289248 c.-7T>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.22
Rv2752c 3065479 p.Phe238Ser missense_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.72
fbiD 3339744 c.627A>C synonymous_variant 0.5
rpoA 3878609 c.-102T>G upstream_gene_variant 0.22
rpoA 3878613 c.-106A>C upstream_gene_variant 0.33
rpoA 3878618 c.-111A>C upstream_gene_variant 0.25
rpoA 3878641 c.-134C>G upstream_gene_variant 0.62
clpC1 4039889 c.816G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.29
embB 4249732 c.3219C>G synonymous_variant 1.0
ethR 4327826 p.Asn93Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407627 c.575delG frameshift_variant 1.0