TB-Profiler result

Run: ERR4799059

Summary

Run ID: ERR4799059

Sample name:

Date: 01-04-2023 08:50:16

Number of reads: 2188754

Percentage reads mapped: 99.51

Strain: lineage4.1.2.1

Drug-resistance: Pre-XDR-TB


Download CSV Download TXT Download PDF Download JSON
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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 0.97
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.98
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.Asp94Tyr missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761004 p.Thr400Ala missense_variant 1.0 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289058 p.Pro62Ser missense_variant 0.97 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
embB 4247574 p.Asp354Ala missense_variant 0.99 ethambutol
ethA 4327333 c.140delT frameshift_variant 1.0 ethionamide, ethionamide
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 0.97
mshA 575679 p.Asn111Ser missense_variant 0.97
rpoB 760115 c.309C>T synonymous_variant 0.95
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
Rv1258c 1407079 c.261delC frameshift_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475222 n.1565G>A non_coding_transcript_exon_variant 1.0
rpsA 1833673 c.132C>T synonymous_variant 0.98
rpsA 1833674 p.Lys45Glu missense_variant 0.98
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 0.98
thyA 3073855 p.Cys206Tyr missense_variant 0.14
thyA 3074182 p.Gln97Arg missense_variant 0.31
thyA 3074323 p.Val50Ala missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448751 p.Gln83Pro missense_variant 0.43
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568759 c.-80A>C upstream_gene_variant 1.0
alr 3840259 p.Tyr388Asp missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.95
ethR 4327918 p.Gly124Cys missense_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0