TB-Profiler result

Run: ERR9029854
Summary

Run ID: ERR9029854

Sample name:

Date: 02-04-2023 09:22:35

Number of reads: 5342325

Percentage reads mapped: 95.58

Strain: lineage4.3.3

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 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 7570 p.Ala90Val missense_variant 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761004 p.Thr400Ala missense_variant 0.96 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.96 rifampicin
rpsL 781822 p.Lys88Thr missense_variant 0.95 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.32
rpoB 761880 p.Ala692Thr missense_variant 0.95
rpoC 764995 c.1626C>G synonymous_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 1472953 n.1108G>A non_coding_transcript_exon_variant 0.17
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.17
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.17
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.16
rrs 1472970 n.1125C>A non_coding_transcript_exon_variant 0.16
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.16
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.16
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.16
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.16
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.16
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.16
rrs 1473001 n.1156G>C non_coding_transcript_exon_variant 0.15
rrs 1473002 n.1157G>A non_coding_transcript_exon_variant 0.15
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.19
rrs 1473008 n.1163C>T non_coding_transcript_exon_variant 0.15
rrs 1473009 n.1164T>G non_coding_transcript_exon_variant 0.15
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.15
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.1
rpsA 1834836 p.Met432Thr missense_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154459 c.1653C>T synonymous_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407720 c.483C>G synonymous_variant 0.96
gid 4408003 p.Asp67Gly missense_variant 0.99
gid 4408156 p.Leu16Arg missense_variant 1.0