TB-Profiler result

Run: ERR459442
Summary

Run ID: ERR459442

Sample name:

Date: 01-04-2023 06:28:15

Number of reads: 1687106

Percentage reads mapped: 99.58

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.99
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 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.29 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2156093 c.18dupA frameshift_variant 1.0 isoniazid
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 576548 p.Ala401Ser missense_variant 0.18
ccsA 620224 p.Glu112Lys missense_variant 0.15
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918194 c.255C>T synonymous_variant 0.14
tlyA 1918212 c.273A>G synonymous_variant 0.12
PPE35 2170530 p.Ala28Glu missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518889 p.Ala259Thr missense_variant 0.11
Rv2752c 3066994 c.-803A>G upstream_gene_variant 0.12
thyA 3074422 p.Pro17Leu missense_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
embC 4239809 c.-54C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244354 c.1122G>A synonymous_variant 0.12
embA 4244525 c.1293G>T synonymous_variant 0.15
ubiA 4268971 p.Ala288Val missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0