TB-Profiler result

Run: SRR18665464
Summary

Run ID: SRR18665464

Sample name:

Date: 03-04-2023 19:58:45

Number of reads: 1944787

Percentage reads mapped: 99.55

Strain: lineage4.1.1.3

Drug-resistance: MDR-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
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
rpoB 761139 p.His445Cys missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.95 streptomycin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.93 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155167 p.Ser315Thr missense_variant 0.95 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.99 ethambutol
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 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.22
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918145 p.Lys69Ile missense_variant 0.2
katG 2154678 c.1434G>C synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726409 p.Asp73His missense_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.12
Rv3083 3449670 c.1167C>A synonymous_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240642 c.780G>A synonymous_variant 0.94
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246584 p.Arg24Pro missense_variant 0.21
embB 4248319 c.1806A>T synonymous_variant 0.28
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249678 c.3165C>A synonymous_variant 0.96
whiB6 4338505 c.-585_16del frameshift_variant&start_lost 1.0