TB-Profiler result

Run: ERR4822376
Summary

Run ID: ERR4822376

Sample name:

Date: 01-04-2023 17:50:27

Number of reads: 4051681

Percentage reads mapped: 99.58

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
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 0.52 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 0.58 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.45 rifampicin
rpoC 764822 p.Asp485Asn missense_variant 0.45 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.17 kanamycin, capreomycin, aminoglycosides, amikacin
tlyA 1918499 c.564dupG frameshift_variant 0.62 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288846 c.395delG frameshift_variant 0.39 pyrazinamide, pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.48 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.55 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.54 ethambutol
ethA 4326083 c.1390dupG frameshift_variant 0.51 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 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 0.62
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
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 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.21
Rv2752c 3064798 p.Arg465Leu missense_variant 0.47
ald 3086731 c.-89A>G upstream_gene_variant 0.41
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.54
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878580 c.-74delC upstream_gene_variant 0.54
rpoA 3878613 c.-106A>C upstream_gene_variant 0.39
rpoA 3878618 c.-111A>C upstream_gene_variant 0.25
rpoA 3878641 c.-134C>G upstream_gene_variant 0.32
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.47
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.21
embB 4246584 p.Arg24Pro missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 0.44
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