TB-Profiler result

Run: ERR4829770
Summary

Run ID: ERR4829770

Sample name:

Date: 01-04-2023 19:40:25

Number of reads: 1025946

Percentage reads mapped: 98.4

Strain: lineage4.3.1

Drug-resistance: HR-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
lineage4.3.1 Euro-American (LAM) LAM9 None 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 7581 p.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rrs 1472358 n.513C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4326850 c.623delC 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
gyrB 6123 p.Ala295Asp missense_variant 0.17
gyrB 6383 c.1145dupC frameshift_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7568 c.267C>T synonymous_variant 0.1
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575186 c.-161delG upstream_gene_variant 0.22
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.91
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472826 n.981G>T non_coding_transcript_exon_variant 0.15
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.11
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.11
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.11
rrs 1473376 n.1531C>T non_coding_transcript_exon_variant 0.11
rrl 1474090 n.433C>A non_coding_transcript_exon_variant 0.33
rrl 1475158 n.1501C>T non_coding_transcript_exon_variant 0.18
rrl 1476125 n.2468G>A non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154037 p.Ser692Asn missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860600 c.-182A>C upstream_gene_variant 0.25
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448469 c.-35A>G upstream_gene_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568531 p.Arg50Leu missense_variant 1.0
Rv3236c 3612286 c.830dupG frameshift_variant 0.1
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247515 c.1002C>T synonymous_variant 1.0
aftB 4268504 c.333G>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0