TB-Profiler result

Run: SRR5486894
Summary

Run ID: SRR5486894

Sample name:

Date: 04-04-2023 10:32:35

Number of reads: 4435097

Percentage reads mapped: 98.52

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 1.0
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
gyrB 6695 p.Ile486Leu missense_variant 0.74 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289186 p.Leu19Pro missense_variant 1.0 pyrazinamide
ahpC 2726112 c.-81C>T upstream_gene_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326884 p.Ser197* stop_gained 0.56 ethionamide
ethA 4327363 c.110delA frameshift_variant 0.13 ethionamide, ethionamide
ethA 4327461 c.11_12delAC frameshift_variant 0.19 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 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.22
mshA 576482 p.Val379Leu missense_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764817 p.Val483Ala missense_variant 1.0
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840952 p.Lys157Glu missense_variant 0.24
alr 3841356 p.Ser22Leu missense_variant 0.75
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.3
embB 4247028 p.Leu172Arg missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338676 c.-155T>C upstream_gene_variant 1.0
gid 4408103 p.Gly34Trp missense_variant 1.0