TB-Profiler result

Run: SRR23310993
Summary

Run ID: SRR23310993

Sample name:

Date: 14-03-2023 05:59:12

Number of reads: 4956558

Percentage reads mapped: 99.53

Strain: lineage4.2.1

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
lineage4.2 Euro-American H;T;LAM None 0.99
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.99
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 6620 p.Asp461Asn missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.98 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.99 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 0.99 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.99 kanamycin
embB 4247402 p.Ser297Ala missense_variant 0.98 ethambutol
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
gyrA 9647 c.2346C>G synonymous_variant 0.19
fgd1 491247 c.465C>T synonymous_variant 0.99
mshA 576613 c.1266A>C synonymous_variant 0.27
mshA 576616 c.1269G>C synonymous_variant 0.33
ccsA 619969 p.Val27Ile missense_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.24
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
fabG1 1673553 p.Asp38Glu missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.16
pepQ 2860159 p.Ala87Gly missense_variant 0.16
ald 3086742 c.-78A>C upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.72
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.22
rpoA 3877960 p.Val183Gly missense_variant 0.98
rpoA 3878597 c.-90G>C upstream_gene_variant 0.25
rpoA 3878641 c.-134C>G upstream_gene_variant 0.62
embC 4240409 p.Pro183Ala missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243200 c.-32delG upstream_gene_variant 0.99
embB 4246527 p.Ala5Gly missense_variant 0.33
embB 4246529 p.Ser6Arg missense_variant 0.26
embB 4246584 p.Arg24Pro missense_variant 0.31
embB 4248328 c.1815G>C synonymous_variant 0.16
embB 4249594 c.3081G>A synonymous_variant 0.98
ethA 4326632 p.His281Pro missense_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0