TB-Profiler result

Run: ERR2510509
Summary

Run ID: ERR2510509

Sample name:

Date: 31-03-2023 18:47:00

Number of reads: 594804

Percentage reads mapped: 99.58

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 1.0
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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289072 p.His57Pro missense_variant 1.0 pyrazinamide
embB 4248002 p.Gln497Lys missense_variant 1.0 ethambutol
gid 4408100 c.102delG 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
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
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760584 p.Asn260Asp missense_variant 0.82
rpoB 762546 p.His914Tyr missense_variant 0.14
rpoB 763003 p.Glu1066Ala missense_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766623 p.Arg1085Gln missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776667 p.Asp605Gly missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303699 p.Thr257Ala missense_variant 1.0
embR 1416197 p.Thr384Met missense_variant 0.11
embR 1416234 p.Cys372Arg missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833930 p.Val130Gly missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103177 c.-135G>A upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726121 c.-72C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038518 c.2187G>C synonymous_variant 0.11
clpC1 4038858 p.Arg616Pro missense_variant 0.11
clpC1 4040819 c.-115G>A upstream_gene_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244829 p.Phe533Leu missense_variant 0.11
embB 4248356 p.Ser615Thr missense_variant 0.1
embB 4249459 c.2946G>A synonymous_variant 0.12
aftB 4268494 p.Ala115Pro missense_variant 0.12
ubiA 4269308 p.Phe176Leu missense_variant 1.0
ethA 4328363 c.-890A>G upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0