TB-Profiler result

Run: ERR8025552
Summary

Run ID: ERR8025552

Sample name:

Date: 23-05-2023 03:03:12

Number of reads: 2631013

Percentage reads mapped: 99.61

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 (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA c.459_466delCAGGGTGC (1.00), pncA c.459_466delCAGGGTGC (1.00)
Streptomycin R rrs n.514A>C (1.00)
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
Aminoglycosides R rrs n.1401A>G (0.91)
Amikacin R rrs n.1401A>G (0.91)
Capreomycin R rrs n.1401A>G (0.91)
Kanamycin R rrs n.1401A>G (0.91)
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), ethA c.65delA (1.00), ethA c.65delA (1.00), ethR p.Ala95Thr (1.00)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.48)
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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.91 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288775 c.459_466delCAGGGTGC frameshift_variant 1.0 pyrazinamide, pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.48 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327408 c.65delA frameshift_variant 1.0 ethionamide, ethionamide
ethR 4327831 p.Ala95Thr missense_variant 1.0 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
gyrB 5273 p.Tyr12His missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7935 p.Glu212Lys missense_variant 0.12
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
mshA 575913 p.Ala189Asp missense_variant 0.14
mshA 575917 c.570C>T synonymous_variant 0.14
mshA 575986 c.639G>A synonymous_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760628 p.Lys274Asn missense_variant 1.0
rpoB 761396 p.Glu530Asp missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 1.0
rpoC 767103 p.Leu1245Arg missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777611 c.870G>A synonymous_variant 0.17
mmpL5 778474 p.Val3Leu missense_variant 0.12
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304073 c.1143C>T synonymous_variant 0.29
fbiC 1304500 p.Ala524Ser missense_variant 0.11
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103059 c.-17G>A upstream_gene_variant 0.11
katG 2153972 p.Asp714Asn missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155797 p.Met105Ile missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288906 c.336C>T synonymous_variant 0.15
pncA 2289785 c.-544A>G upstream_gene_variant 0.13
kasA 2518582 c.468G>A synonymous_variant 0.13
folC 2747205 c.392_393dupTG frameshift_variant 0.11
thyX 3067304 p.Glu214Asp missense_variant 0.12
thyX 3067946 c.-1C>T upstream_gene_variant 0.17
thyX 3067988 c.-43A>C upstream_gene_variant 0.3
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339032 c.-86C>T upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841029 p.Ala131Val missense_variant 0.25
clpC1 4038745 p.Thr654Ala missense_variant 0.12
embC 4240793 p.Ala311Thr missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244055 p.Gly275Ser missense_variant 0.14
embA 4245529 p.Gly766Asp missense_variant 0.11
embA 4245955 c.2727delG frameshift_variant 0.14
aftB 4267060 p.His593Tyr missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4326598 c.-951T>A upstream_gene_variant 0.17
ethA 4327454 p.Val7Ala missense_variant 0.1
whiB6 4338296 p.Trp76Gly missense_variant 0.36
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