TB-Profiler result

Run: ERR8774466
Summary

Run ID: ERR8774466

Sample name:

Date: 02-04-2023 08:31:09

Number of reads: 731833

Percentage reads mapped: 99.34

Strain: lineage4.1.2.1

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
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288839 p.Thr135Pro missense_variant 1.0 pyrazinamide
ahpC 2726136 c.-57C>T upstream_gene_variant 1.0 isoniazid
ethA 4326613 c.860delA frameshift_variant 1.0 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 7731 p.Glu144Lys missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760920 p.Leu372Met missense_variant 0.12
rpoB 761321 p.Phe505Leu missense_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766488 p.Pro1040Arg 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
rrs 1472130 n.285G>T non_coding_transcript_exon_variant 0.13
rrl 1475206 n.1549C>A non_coding_transcript_exon_variant 0.25
rrl 1476714 n.3057G>T non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2221988 p.Leu393Ile missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518734 p.Ile207Thr missense_variant 0.12
kasA 2518775 p.Asp221Tyr missense_variant 0.17
ahpC 2725922 c.-271G>T upstream_gene_variant 0.13
Rv2752c 3065975 p.Asp73Tyr missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086819 c.-1C>A upstream_gene_variant 0.16
Rv3083 3449070 c.567G>T synonymous_variant 0.25
Rv3083 3449079 p.Leu192Phe missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474348 c.342C>A synonymous_variant 0.21
fbiA 3641060 p.Trp173Leu missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ethA 4327075 p.Phe133Leu missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0