TB-Profiler result

Run: ERR176605

Summary

Run ID: ERR176605

Sample name:

Date: 20-10-2023 22:21:29

Number of reads: 4195489

Percentage reads mapped: 95.8

Strain: lineage4.3.4.2.1

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
Rifampicin
Isoniazid R katG p.Ser315Asn (0.99)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.98)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
katG 2155168 p.Ser315Asn missense_variant 0.99 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
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_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
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.12
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.13
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.14
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.13
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.11
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.13
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.13
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.14
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.15
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.17
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.16
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.15
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.14
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.11
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.13
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.13
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.14
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.1
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.12
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.12
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.15
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102776 c.267C>T synonymous_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.99