TB-Profiler result

Run: SRR1173523
Summary

Run ID: SRR1173523

Sample name:

Date: 03-04-2023 03:26:42

Number of reads: 375724

Percentage reads mapped: 95.25

Strain: lineage4

Drug-resistance: MDR-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
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
rpoB 761155 p.Ser450Leu missense_variant 0.8 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289067 p.Ser59Pro missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 6815 p.Lys526Gln missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8969 c.1668G>T synonymous_variant 0.2
rpoC 764095 c.726C>T synonymous_variant 0.5
rpoC 764810 p.Pro481Thr missense_variant 0.4
rpoC 766485 p.Val1039Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776189 p.Met764Ile missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472863 n.1018T>A non_coding_transcript_exon_variant 0.22
rrs 1473078 n.1233G>T non_coding_transcript_exon_variant 0.29
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.29
rrl 1473991 n.334C>T non_coding_transcript_exon_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
inhA 1674681 p.Trp160Cys missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222015 p.Val384Leu missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065765 p.Tyr143His missense_variant 0.33
thyX 3067222 p.Ala242Ser missense_variant 0.4
fprA 3475062 c.1056C>A synonymous_variant 0.33
alr 3840764 c.657G>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244756 p.Glu508Asp missense_variant 0.2
embA 4244933 c.1701A>C synonymous_variant 0.18
embA 4245767 p.Glu845Asp missense_variant 0.25
ethR 4327144 c.-405C>G upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0