TB-Profiler result

Run: ERR2433013
Summary

Run ID: ERR2433013

Sample name:

Date: 31-03-2023 18:12:08

Number of reads: 630329

Percentage reads mapped: 99.84

Strain: lineage4.3.4.2.1

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
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761140 p.His445Arg missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289186 p.Leu19Arg missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4326302 p.Trp391* stop_gained 1.0 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
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8795 c.1494C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778854 p.Val18Ile missense_variant 0.1
mmpS5 779609 c.-704C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304696 p.Trp589* stop_gained 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156064 c.48T>C synonymous_variant 0.11
katG 2156268 c.-157G>A upstream_gene_variant 0.1
PPE35 2170688 c.-76G>A upstream_gene_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289909 c.-668G>A upstream_gene_variant 1.0
ahpC 2726000 c.-193T>C upstream_gene_variant 0.1
ribD 2986908 p.Thr24Ala missense_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449003 p.Gln167Arg missense_variant 0.11
Rv3083 3449636 c.1135delG frameshift_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840704 c.717A>G synonymous_variant 0.1
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3878310 c.198G>T synonymous_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246823 p.Lys104* stop_gained 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408093 p.Gly37Ala missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0