TB-Profiler result

Run: SRR16088412

Summary

Run ID: SRR16088412

Sample name:

Date: 12-01-2024 22:35:26

Number of reads: 3871909

Percentage reads mapped: 99.6

Strain: lineage2.2.1

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
Rifampicin R rpoB p.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (0.54), katG p.Ser315Thr (0.45)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA c.355dupT (0.47), pncA c.355dupT (0.47)
Streptomycin R rpsL p.Lys43Arg (0.50), rpsL p.Lys88Arg (0.45)
Fluoroquinolones R gyrA p.Gly88Ala (0.50), gyrA p.Asp94Gly (0.48)
Moxifloxacin R gyrA p.Gly88Ala (0.50), gyrA p.Asp94Gly (0.48)
Ofloxacin R gyrA p.Gly88Ala (0.50), gyrA p.Asp94Gly (0.48)
Levofloxacin R gyrA p.Gly88Ala (0.50), gyrA p.Asp94Gly (0.48)
Ciprofloxacin R gyrA p.Gly88Ala (0.50), gyrA p.Asp94Gly (0.48)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (0.54)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.54)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 7564 p.Gly88Ala missense_variant 0.5 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.48 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.5 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.45 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.54 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.45 isoniazid
pncA 2288886 c.355dupT frameshift_variant 0.47 pyrazinamide, pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.54 kanamycin
embB 4247429 p.Met306Val missense_variant 1.0 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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762477 p.Lys891Glu missense_variant 0.48
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765462 p.Asn698Ser missense_variant 0.53
rpoC 766645 p.Glu1092Asp missense_variant 0.59
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834427 p.Ile296Val missense_variant 0.51
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156100 c.12A>G synonymous_variant 0.48
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223106 p.Val20Ala missense_variant 0.53
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 0.57
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568736 c.-57T>G upstream_gene_variant 0.48
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
panD 4043867 p.Gly139* stop_gained 0.54
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.51
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 0.41
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0