TB-Profiler result

Run: ERR11243529
Summary

Run ID: ERR11243529

Sample name:

Date: 21-04-2023 21:09:03

Number of reads: 1158355

Percentage reads mapped: 99.4

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 inhA c.-154G>A (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embA c.-12C>T (1.00), embB p.Gly406Ala (1.00)
Pyrazinamide R pncA p.Thr47Ala (1.00)
Streptomycin R rrs n.517C>T (1.00)
Fluoroquinolones R gyrA p.Ala90Val (1.00)
Moxifloxacin R gyrA p.Ala90Val (1.00)
Ofloxacin R gyrA p.Ala90Val (1.00)
Levofloxacin R gyrA p.Ala90Val (1.00)
Ciprofloxacin R gyrA p.Ala90Val (1.00)
Aminoglycosides
Amikacin R eis c.-14C>T (1.00)
Capreomycin
Kanamycin R eis c.-14C>T (1.00)
Cycloserine
Ethionamide R inhA c.-154G>A (1.00), ethA c.768delG (1.00), ethA c.768delG (1.00)
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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289103 p.Thr47Ala missense_variant 1.0 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4326705 c.768delG frameshift_variant 1.0 ethionamide, 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 491742 c.960T>C synonymous_variant 1.0
mshA 575378 p.Gly11Trp missense_variant 0.23
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576217 p.Leu290Phe missense_variant 0.33
mshA 576344 p.His333Asn missense_variant 0.19
ccsA 620224 p.Glu112* stop_gained 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620725 p.Leu279Met missense_variant 0.33
rpoB 761527 p.Asp574Gly missense_variant 0.12
rpoB 762286 p.Arg827Leu missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
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
fbiC 1303425 c.495G>T synonymous_variant 0.17
fbiC 1304658 c.1728C>A synonymous_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476171 n.2514G>T non_coding_transcript_exon_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917816 c.-124G>T upstream_gene_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.94
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170066 p.Ala183Thr missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746968 p.Gly211Trp missense_variant 0.2
folC 2747542 c.57C>A synonymous_variant 0.23
thyX 3067313 c.633G>T synonymous_variant 0.2
thyX 3067378 c.568C>A synonymous_variant 0.2
ald 3086695 c.-125C>T upstream_gene_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339721 p.Gly202Trp missense_variant 0.25
Rv3083 3449472 c.969C>A synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475356 c.1350G>T synonymous_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613103 p.Arg5Met missense_variant 0.16
fbiB 3641705 p.Glu57Asp missense_variant 0.18
alr 3841453 c.-33G>T upstream_gene_variant 0.18
clpC1 4038875 c.1830C>A synonymous_variant 0.43
clpC1 4039013 p.Lys564Asn missense_variant 0.17
embC 4240457 p.Gly199Trp missense_variant 0.18
embC 4241177 p.Gly439Trp missense_variant 0.2
embC 4241688 p.Thr609Lys missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243032 p.Trp1057Leu missense_variant 0.38
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244851 p.Arg540Leu missense_variant 0.25
embB 4247500 c.987C>A synonymous_variant 0.18
embB 4248506 p.Gly665Trp missense_variant 0.19
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338421 p.Cys34Tyr missense_variant 1.0
whiB6 4338563 c.-42G>T upstream_gene_variant 1.0
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