TB-Profiler result

Run: ERR4812820
Summary

Run ID: ERR4812820

Sample name:

Date: 01-04-2023 12:21:28

Number of reads: 573295

Percentage reads mapped: 99.41

Strain:

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
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.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val 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 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2154022 c.2089delG frameshift_variant 0.12 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289090 p.His51Arg missense_variant 0.14 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 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
rpoB 762991 p.Phe1062Cys missense_variant 0.42
rpoC 763031 c.-339T>C upstream_gene_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
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779630 c.-725T>C upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302814 c.-117C>A upstream_gene_variant 0.12
Rv1258c 1406753 c.588C>T synonymous_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476178 n.2521C>A non_coding_transcript_exon_variant 0.1
rpsA 1833583 c.42C>T synonymous_variant 0.1
rpsA 1834177 c.636A>C 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
pncA 2288886 p.Trp119Leu missense_variant 1.0
kasA 2518325 p.His71Asp missense_variant 0.2
Rv2752c 3066110 p.Gly28Ser missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087662 c.844delA frameshift_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568554 c.126G>T synonymous_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
panD 4044088 p.Gly65Asp missense_variant 0.1
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248087 p.Tyr525Cys missense_variant 0.11
aftB 4268770 p.Gln23* stop_gained 0.14
ethA 4326362 p.Gly371Val missense_variant 1.0
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