TB-Profiler result

Run: SRR1173580
Summary

Run ID: SRR1173580

Sample name:

Date: 03-04-2023 03:28:09

Number of reads: 1636515

Percentage reads mapped: 96.49

Strain: lineage4.8

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
lineage4.8 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
pncA 2288988 p.Leu85Pro missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_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 6756 p.Ile506Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 766488 p.Pro1040Arg missense_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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155259 p.Gly285Ser missense_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168179 p.Pro812Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.31
PPE35 2169866 c.747G>C synonymous_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067464 p.Ile161Thr missense_variant 1.0
ald 3087036 p.Lys73Glu missense_variant 0.97
embC 4242425 p.Arg855Gly missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248024 p.Glu504Gly missense_variant 1.0
embB 4249354 c.2841G>C synonymous_variant 0.96
ubiA 4269140 p.Cys232Gly missense_variant 1.0
whiB6 4338414 c.107_108insT frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338598 c.-77G>C upstream_gene_variant 1.0
gid 4408168 p.Phe12Cys missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0