TB-Profiler result

Run: ERR11067627
Summary

Run ID: ERR11067627

Sample name:

Date: 05-04-2023 02:52:05

Number of reads: 3380839

Percentage reads mapped: 99.54

Strain: lineage2.2.1

Drug-resistance: 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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rplC 801268 p.Cys154Arg missense_variant 1.0 linezolid
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.99 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288848 p.Gly132Ser missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4324386 c.-95_*1617del transcript_ablation 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
mshA 576108 p.Ala254Gly missense_variant 0.29
mshA 576456 p.Val370Gly missense_variant 0.55
mshA 576483 p.Val379Gly missense_variant 0.4
mshA 576606 p.Ala420Gly missense_variant 0.27
mshA 576613 c.1266A>C synonymous_variant 0.73
mshA 576616 c.1269G>C synonymous_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.2
rpoC 764817 p.Val483Gly missense_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
mmpL5 777883 p.Gly200Arg missense_variant 0.4
mmpR5 779130 c.144dupC frameshift_variant 1.0
mmpR5 779311 p.Ile108Val 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 1303157 p.His76Pro missense_variant 0.3
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918621 p.Ser228Arg missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170035 p.Val193Gly missense_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.3
thyX 3067958 c.-13T>G upstream_gene_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087012 c.196dupG frameshift_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.71
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878580 c.-73A>C upstream_gene_variant 0.29
rpoA 3878641 c.-134C>G upstream_gene_variant 0.89
clpC1 4040550 p.Leu52Trp missense_variant 0.19
embC 4240409 p.Pro183Ala missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243682 c.450T>G synonymous_variant 0.22
embB 4246527 p.Ala5Gly missense_variant 0.59
embB 4247016 p.Ser168Trp missense_variant 0.42
embB 4247020 c.507C>G synonymous_variant 0.8
embB 4247028 p.Leu172Arg missense_variant 0.5
embB 4247033 p.Ser174Arg missense_variant 0.43
embB 4248328 c.1815G>C synonymous_variant 0.16
aftB 4267400 c.1437G>C synonymous_variant 0.28
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338200 p.Asp108His missense_variant 0.23
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