TB-Profiler result

Run: ERR9806947
Summary

Run ID: ERR9806947

Sample name:

Date: 21-05-2023 05:50:45

Number of reads: 2686872

Percentage reads mapped: 99.57

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.His445Arg (1.00), rpoB p.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Asp8Asn (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 (0.95)
Amikacin R rrs n.1401A>G (0.95)
Capreomycin R rrs n.1401A>G (0.95)
Kanamycin R rrs n.1401A>G (0.95)
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (1.00), ethR p.Ala95Thr (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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761140 p.His445Arg missense_variant 1.0 rifampicin
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 0.95 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
pncA 2289220 p.Asp8Asn missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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
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 760385 c.579G>A synonymous_variant 0.12
rpoB 760487 c.681G>A synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 1.0
rpoC 765522 p.Asp718Gly missense_variant 0.11
rpoC 766900 c.3531T>C synonymous_variant 0.14
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 778215 p.Ser89Asn missense_variant 0.12
mmpL5 778348 p.Val45Phe missense_variant 0.11
mmpS5 778734 p.Tyr58His missense_variant 0.11
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 1304010 p.Leu360Phe missense_variant 0.12
Rv1258c 1406293 p.Gly350Trp missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406991 p.Gly117Val missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674506 p.Gly102Val missense_variant 0.13
rpsA 1833512 c.-29delC upstream_gene_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102834 p.Pro70Gln missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290008 c.-769_-768delGA upstream_gene_variant 0.15
kasA 2519289 p.Gly392Val missense_variant 0.11
eis 2715310 p.Pro8Gln missense_variant 0.16
Rv2752c 3064567 p.Gly542Val missense_variant 0.18
Rv2752c 3064656 p.Glu512Asp missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087721 p.Met301Thr missense_variant 1.0
Rv3083 3448550 p.Gly16Asp missense_variant 0.12
Rv3083 3449743 p.Ala414Thr missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474033 c.27G>T synonymous_variant 0.12
Rv3236c 3612034 c.1083C>A synonymous_variant 0.13
Rv3236c 3612086 p.Ala344Asp missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642138 p.Ala202Thr missense_variant 0.18
embA 4242550 c.-683C>A upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243236 p.Pro2Thr missense_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244171 c.939G>A synonymous_variant 0.11
embA 4245339 p.Gly703Cys missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268160 p.Ile226Thr missense_variant 0.1
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