TB-Profiler result

Run: SRR24114350

Summary

Run ID: SRR24114350

Sample name:

Date: 16-04-2023 21:03:00

Number of reads: 5029634

Percentage reads mapped: 99.65

Strain: lineage3

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.His445Tyr (0.24), rpoB p.Leu452Pro (0.80)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol
Pyrazinamide
Streptomycin R gid p.Glu92* (0.31)
Fluoroquinolones R gyrA p.Asp89Asn (0.61)
Moxifloxacin R gyrA p.Asp89Asn (0.61)
Ofloxacin R gyrA p.Asp89Asn (0.61)
Levofloxacin R gyrA p.Asp89Asn (0.61)
Ciprofloxacin R gyrA p.Asp89Asn (0.61)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 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 7566 p.Asp89Asn missense_variant 0.61 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 0.24 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.8 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4407929 p.Glu92* stop_gained 0.31 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 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.24
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801044 p.Arg79Leu missense_variant 0.36
embR 1416814 c.534G>A synonymous_variant 0.37
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.35
rrl 1476201 n.2544C>G non_coding_transcript_exon_variant 0.75
fabG1 1673553 p.Asp38Glu missense_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.33
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.28
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 0.59
fbiD 3339734 p.Ala206Gly missense_variant 0.52
fbiD 3339751 p.Ala212Pro missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.25
whiB7 3568431 c.249C>G synonymous_variant 0.19
whiB7 3568857 c.-178C>T upstream_gene_variant 0.34
fbiB 3642877 p.Lys448Arg missense_variant 0.67
rpoA 3878618 c.-111A>C upstream_gene_variant 0.2
rpoA 3878641 c.-134C>G upstream_gene_variant 0.37
panD 4044023 c.259C>T synonymous_variant 0.44
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.16
embB 4246777 c.264G>T synonymous_variant 0.3
aftB 4267424 c.1413G>T synonymous_variant 0.41
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0