TB-Profiler result

Run: ERR9806989
Summary

Run ID: ERR9806989

Sample name:

Date: 21-05-2023 07:03:47

Number of reads: 2386010

Percentage reads mapped: 99.54

Strain: lineage4.1.1

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
Rifampicin R rpoB p.Gln432Lys (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide
Streptomycin R gid c.386delG (1.00)
Fluoroquinolones R gyrA p.Asp94Asn (1.00)
Moxifloxacin R gyrA p.Asp94Asn (1.00)
Ofloxacin R gyrA p.Asp94Asn (1.00)
Levofloxacin R gyrA p.Asp94Asn (1.00)
Ciprofloxacin R gyrA p.Asp94Asn (1.00)
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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 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 7581 p.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761100 p.Gln432Lys missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4407816 c.386delG frameshift_variant 1.0 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
gyrB 6971 p.Pro578Ala 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
ccsA 620094 c.204G>A synonymous_variant 0.14
rpoB 759836 c.30C>A synonymous_variant 0.11
rpoB 760196 c.390C>T synonymous_variant 1.0
rpoB 760334 c.528G>A synonymous_variant 0.13
rpoB 762056 c.2250G>A synonymous_variant 0.1
rpoB 762285 p.Arg827Ser missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 0.9
rpoC 766627 c.3258G>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775838 c.2643G>A synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303977 c.1047C>T synonymous_variant 0.11
fbiC 1304142 c.1212G>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473326 n.1481G>A non_coding_transcript_exon_variant 0.15
rpsA 1833503 c.-39G>A upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155428 c.684C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726210 c.18T>C synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087164 c.346delG frameshift_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474469 p.Asn155Asp missense_variant 0.11
whiB7 3568635 c.45G>A synonymous_variant 0.15
fbiA 3641447 p.Thr302Met missense_variant 1.0
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3877603 p.His302Arg missense_variant 0.11
rpoA 3878601 c.-95delG upstream_gene_variant 0.44
rpoA 3878613 c.-113_-107delCAACCCA upstream_gene_variant 0.35
clpC1 4039342 c.1362dupG frameshift_variant 0.11
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4241125 c.1263G>A synonymous_variant 0.15
embA 4242491 c.-742C>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267976 c.861G>A synonymous_variant 0.13
ubiA 4269140 p.Cys232Ser missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407600 c.603C>T synonymous_variant 0.12