TB-Profiler result

Run: SRR18714762
Summary

Run ID: SRR18714762

Sample name:

Date: 03-04-2023 20:03:07

Number of reads: 2979090

Percentage reads mapped: 99.61

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, 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
mshA 576606 p.Ala420Gly missense_variant 0.23
mshA 576613 c.1266A>C synonymous_variant 0.62
rpoC 764367 p.Gly333Ala missense_variant 0.18
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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.99
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.21
fabG1 1673553 p.Asp38Glu missense_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153942 p.Phe724Val missense_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.23
thyA 3074422 p.Pro17Leu missense_variant 1.0
ald 3087816 p.Cys333Gly missense_variant 0.17
fbiD 3339734 p.Ala206Gly missense_variant 0.67
fbiD 3339751 p.Ala212Pro missense_variant 0.24
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
rpoA 3878597 c.-90G>C upstream_gene_variant 0.45
rpoA 3878641 c.-134C>G upstream_gene_variant 0.64
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246529 p.Ser6Arg missense_variant 0.2
embB 4246584 p.Arg24Pro missense_variant 0.12
embB 4247028 p.Leu172Arg missense_variant 0.21
embB 4248328 c.1815G>C synonymous_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408102 p.Gly34Glu missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0