TB-Profiler result

Run: SRR18337386
Summary

Run ID: SRR18337386

Sample name:

Date: 03-04-2023 19:37:26

Number of reads: 974769

Percentage reads mapped: 99.7

Strain: lineage4.8

Drug-resistance: Other

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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
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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 576108 p.Ala254Gly missense_variant 0.39
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777299 c.1182G>A synonymous_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472433 n.588G>A non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474905 n.1248T>A non_coding_transcript_exon_variant 0.11
rrl 1476057 n.2400T>A non_coding_transcript_exon_variant 0.17
rrl 1476127 n.2470C>A non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222812 p.Leu118* stop_gained 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726182 c.-11T>A upstream_gene_variant 0.12
ahpC 2726774 c.582G>A synonymous_variant 0.15
alr 3840764 c.657G>C synonymous_variant 1.0
clpC1 4038753 p.Gln651Arg missense_variant 0.1
embC 4242497 p.Arg879Gly missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.15
embB 4246555 c.42G>C synonymous_variant 0.22
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4246563 p.Leu17Trp missense_variant 0.18
embB 4246567 c.54G>T synonymous_variant 0.18
embB 4246613 p.Gly34Arg missense_variant 0.12
embB 4249107 p.Leu865Gln missense_variant 0.12
ethR 4327354 c.-195G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0