TB-Profiler result

Run: SRR23310995

Summary

Run ID: SRR23310995

Sample name:

Date: 14-03-2023 06:05:01

Number of reads: 4014333

Percentage reads mapped: 99.61

Strain: lineage2.2

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 0.99
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 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289225 p.Ile6Thr missense_variant 0.99 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.99 ethambutol
ethA 4327363 c.107delA 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 0.99
fgd1 491742 c.960T>C synonymous_variant 0.99
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576613 c.1266A>C synonymous_variant 0.38
mshA 576615 p.Arg423Pro missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 765461 p.Asn698His missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 0.98
mmpL5 777883 p.Gly200Arg missense_variant 0.17
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
inhA 1673405 c.-796delC upstream_gene_variant 0.99
fabG1 1673553 p.Asp38Glu missense_variant 0.26
rpsA 1834177 c.636A>C synonymous_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2170065 p.Ala183Gly missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.16
pepQ 2860159 p.Ala87Gly missense_variant 0.27
ald 3086731 c.-89A>G upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.76
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
fprA 3474584 p.Glu193Ala missense_variant 0.97
whiB7 3568428 c.252A>G synonymous_variant 0.26
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878597 c.-90G>C upstream_gene_variant 0.31
rpoA 3878613 c.-106A>C upstream_gene_variant 0.33
rpoA 3878641 c.-134C>G upstream_gene_variant 0.8
embC 4240409 p.Pro183Ala missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.99
embA 4243460 c.228C>T synonymous_variant 0.98
embB 4246527 p.Ala5Gly missense_variant 0.33
embB 4248328 c.1815G>C synonymous_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 0.99
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