TB-Profiler result

Run: ERR9029872
Summary

Run ID: ERR9029872

Sample name:

Date: 02-04-2023 09:23:32

Number of reads: 6548440

Percentage reads mapped: 99.77

Strain: lineage4.3.4.2;lineage4.1.1.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.73
lineage4.1 Euro-American T;X;H None 0.25
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.28
lineage4.3.4 Euro-American (LAM) LAM RD174 0.77
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.25
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.77
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.Asp94Gly missense_variant 0.23 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.26 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288883 p.Leu120Pro missense_variant 0.31 pyrazinamide
ald 3087810 c.992dupC frameshift_variant 0.24 cycloserine
embB 4247431 p.Met306Ile missense_variant 0.73 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.28 ethambutol
ethA 4326183 c.1290delC frameshift_variant 0.27 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
gyrB 6140 p.Val301Leu missense_variant 0.72
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 0.32
rpoC 764817 p.Val483Ala missense_variant 0.35
rpoC 764918 p.Val517Leu missense_variant 0.64
rpoC 764995 c.1626C>G synonymous_variant 0.7
rpoC 765150 p.Gly594Glu missense_variant 0.3
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302954 c.24G>A synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833469 c.-73G>T upstream_gene_variant 0.75
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154678 c.1434G>C synonymous_variant 0.23
PPE35 2169405 p.Asn403Ser missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726409 p.Asp73His missense_variant 0.29
ribD 2986827 c.-12G>A upstream_gene_variant 0.22
thyA 3073868 p.Thr202Ala missense_variant 0.72
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449437 c.936_942delCGCGGCG frameshift_variant 0.28
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.86
alr 3840719 c.702A>G synonymous_variant 0.88
clpC1 4038287 c.2418C>T synonymous_variant 0.78
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.26
embB 4249408 c.2895G>A synonymous_variant 0.26
embB 4249678 c.3165C>A synonymous_variant 0.32
whiB6 4338247 p.Leu92Ser missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407934 p.Leu90Arg missense_variant 0.27
gid 4407970 p.Pro78Leu missense_variant 0.72
gid 4408156 p.Leu16Arg missense_variant 0.76