TB-Profiler result

Run: ERR12268442
Summary

Run ID: ERR12268442

Sample name:

Date: 09-01-2024 14:42:28

Number of reads: 1959918

Percentage reads mapped: 97.38

Strain: lineage4.1.2.1

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
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys88Gln (0.91)
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 781821 p.Lys88Gln missense_variant 0.91 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8987 c.1686C>G synonymous_variant 0.12
gyrA 8990 c.1689C>G synonymous_variant 0.12
gyrA 8996 c.1695T>C synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9335 c.2034G>C synonymous_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 0.93
rpoB 761645 c.1839C>G synonymous_variant 0.12
rpoC 764752 c.1383G>C synonymous_variant 0.13
rpoC 764827 c.1458G>C synonymous_variant 0.12
rpoC 764858 c.1489T>C synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781865 c.306G>C synonymous_variant 0.12
rpsL 781868 c.309T>C synonymous_variant 0.12
rpsL 781877 c.318T>C synonymous_variant 0.12
rpsL 781898 c.339A>T synonymous_variant 0.12
rpsL 781916 c.357T>C synonymous_variant 0.13
rplC 800612 c.-197A>G upstream_gene_variant 0.18
rplC 800618 c.-191T>C upstream_gene_variant 0.18
rplC 800627 c.-182C>T upstream_gene_variant 0.17
rplC 800648 c.-161A>T upstream_gene_variant 0.2
rplC 800654 c.-155T>C upstream_gene_variant 0.19
rplC 800693 c.-116A>G upstream_gene_variant 0.18
rplC 800703 c.-106T>C upstream_gene_variant 0.19
rplC 800715 c.-94A>C upstream_gene_variant 0.19
rplC 800720 c.-89T>C upstream_gene_variant 0.2
rplC 800723 c.-86C>G upstream_gene_variant 0.19
rplC 800844 c.36T>C synonymous_variant 0.16
rplC 800865 c.57A>G synonymous_variant 0.12
rplC 800867 p.Ser20Asn missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.16
inhA 1674537 c.336C>G synonymous_variant 0.13
inhA 1674542 p.Ala114Glu missense_variant 0.12
inhA 1674546 c.345T>C synonymous_variant 0.12
inhA 1674561 c.360C>T synonymous_variant 0.12
inhA 1674582 c.381T>C synonymous_variant 0.13
inhA 1674585 c.384T>C synonymous_variant 0.14
inhA 1674589 p.Met130Leu missense_variant 0.14
inhA 1674597 c.396G>A synonymous_variant 0.13
inhA 1674601 p.Leu134Thr missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038683 c.2022T>C synonymous_variant 0.14
clpC1 4038695 c.2010C>G synonymous_variant 0.13
clpC1 4038770 c.1935C>T synonymous_variant 0.12
clpC1 4038773 c.1932T>C synonymous_variant 0.12
clpC1 4038782 c.1923G>C synonymous_variant 0.13
clpC1 4038812 c.1893T>C synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0