TB-Profiler result

Run: ERR4799222
Summary

Run ID: ERR4799222

Sample name:

Date: 01-04-2023 08:57:44

Number of reads: 2792066

Percentage reads mapped: 99.65

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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 7581 p.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.97 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.38 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.56 isoniazid, ethionamide
fabG1 1673432 c.-8T>C upstream_gene_variant 0.42 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.66 kanamycin
thyX 3067961 c.-16C>T upstream_gene_variant 0.42 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.99 ethambutol
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
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766488 p.Pro1040Arg missense_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpS5 779615 c.-710C>G upstream_gene_variant 0.96
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473962 n.305T>G non_coding_transcript_exon_variant 0.12
rrl 1473969 n.312G>T non_coding_transcript_exon_variant 0.15
rrl 1474026 n.369C>A non_coding_transcript_exon_variant 0.14
rrl 1475627 n.1970G>T non_coding_transcript_exon_variant 0.15
rrl 1476402 n.2745C>A non_coding_transcript_exon_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 0.97
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067949 c.-4C>T upstream_gene_variant 0.61
thyA 3074243 c.228dupA frameshift_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.97
aftB 4267647 p.Asp397Gly missense_variant 0.98
ethA 4326676 p.Ser266Arg missense_variant 0.98
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
ethA 4325180 c.1261_*823del stop_lost&conservative_inframe_deletion&splice_region_variant 1.0