TB-Profiler result

Run: SRR23861893
Summary

Run ID: SRR23861893

Sample name:

Date: 12-04-2023 08:58:10

Number of reads: 3396882

Percentage reads mapped: 99.54

Strain: lineage4.1.2.1

Drug-resistance: RR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Ala (0.15)
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
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 0.98
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
rpoB 761154 p.Ser450Ala missense_variant 0.15 rifampicin
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576093 p.Pro249Arg missense_variant 0.16
mshA 576100 p.Asp251Glu missense_variant 0.12
mshA 576113 p.Arg256Gly missense_variant 0.15
mshA 576116 p.Ala257Pro missense_variant 0.23
rpoB 760106 c.300G>A synonymous_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339739 p.Ala208Pro missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568401 c.279G>T stop_lost&splice_region_variant 0.12
whiB7 3568418 p.Lys88Gln missense_variant 0.22
whiB7 3568420 p.Arg87Pro missense_variant 0.18
whiB7 3568422 c.258G>C synonymous_variant 0.19
whiB7 3568428 c.252A>C synonymous_variant 0.18
whiB7 3568431 c.249C>G synonymous_variant 0.19
clpC1 4040235 p.Gly157Ala missense_variant 0.18
clpC1 4040242 p.Thr155Pro missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246536 p.Arg8Pro missense_variant 0.14
embB 4246542 p.Ser10Thr missense_variant 0.25
embB 4246552 p.Asn13Lys missense_variant 0.19
embB 4246559 p.Ile16Leu missense_variant 0.21
embB 4246574 p.Ala21Ser missense_variant 0.26
embB 4246609 c.96C>A synonymous_variant 0.17
embB 4247013 p.Pro167Arg missense_variant 0.15
embB 4247016 p.Ser168Trp missense_variant 0.16
ethA 4326226 c.1248C>G synonymous_variant 0.14
ethA 4326238 p.Asn412Lys missense_variant 0.14
ethA 4328025 c.-552T>A upstream_gene_variant 0.15
ethR 4328030 p.Ala161Gly missense_variant 0.23
ethR 4328041 p.Thr165Pro missense_variant 0.14
ethR 4328045 p.Leu166Gln missense_variant 0.17
whiB6 4338513 c.9C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0