TB-Profiler result

Run: ERR1213870
Summary

Run ID: ERR1213870

Sample name:

Date: 31-03-2023 12:42:02

Number of reads: 1749227

Percentage reads mapped: 99.34

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 0.99
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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 761108 p.Met434Ile missense_variant 0.12 rifampicin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288820 c.421delC frameshift_variant 1.0 pyrazinamide
folC 2747471 p.Ile43Thr missense_variant 1.0 para-aminosalicylic_acid
ethA 4327077 c.396delA frameshift_variant 1.0 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 9304 p.Gly668Asp missense_variant 1.0
mshA 576534 p.Gly396Asp missense_variant 0.2
rpoC 764584 c.1215G>T synonymous_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765071 p.Pro568Ser missense_variant 0.15
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 1472001 n.156A>G non_coding_transcript_exon_variant 0.11
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.22
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.2
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.2
rrl 1474657 n.1000G>T non_coding_transcript_exon_variant 0.12
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.18
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.27
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.3
fabG1 1673262 c.-178G>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101705 c.1338C>T synonymous_variant 0.12
katG 2156438 c.-327C>T upstream_gene_variant 0.18
Rv1979c 2222374 p.Gly264Asp missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.93
ahpC 2725950 c.-243G>A upstream_gene_variant 0.11
Rv2752c 3065293 p.Val300Ala missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086800 c.-20C>T upstream_gene_variant 1.0
Rv3083 3448630 p.Gly43Ser missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiA 3640681 p.Val47Ile missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_variant 0.9
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245133 p.Trp634Leu missense_variant 0.14
embB 4247884 c.1371C>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0