TB-Profiler result

Run: ERR4799716
Summary

Run ID: ERR4799716

Sample name:

Date: 01-04-2023 09:19:01

Number of reads: 4089915

Percentage reads mapped: 99.47

Strain: lineage4.2.2.2

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
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
lineage4.2 Euro-American H;T;LAM None 0.99
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.98
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.97
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 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2288790 p.Leu151Ser missense_variant 0.98 pyrazinamide
eis 2715347 c.-15C>G upstream_gene_variant 0.99 kanamycin
folC 2747480 p.Glu40Gly missense_variant 0.98 para-aminosalicylic_acid
embB 4247730 p.Gly406Ala missense_variant 0.98 ethambutol
ethA 4327480 c.-7T>C upstream_gene_variant 0.97 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 8688 p.Ala463Ser missense_variant 0.97
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 0.97
rpoB 761489 c.1683G>A synonymous_variant 0.99
rpoC 767123 p.Val1252Met missense_variant 0.98
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.98
ald 3086742 c.-78A>C upstream_gene_variant 0.95
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449765 c.1264delA frameshift_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240327 c.465G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269721 p.Ala38Val missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0