TB-Profiler result

Run: ERR8025547
Summary

Run ID: ERR8025547

Sample name:

Date: 19-05-2023 17:34:10

Number of reads: 2561900

Percentage reads mapped: 99.56

Strain: lineage2.2.2

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
Rifampicin R rpoB p.Asp435Val (1.00)
Isoniazid R fabG1 c.-17G>T (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R rpsA p.Glu433Asp (0.15), pncA c.517dupG (1.00), pncA c.517dupG (1.00)
Streptomycin R rrs n.514A>C (1.00), gid p.Leu79Ser (1.00)
Fluoroquinolones R gyrA p.Asp94Asn (1.00)
Moxifloxacin R gyrA p.Asp94Asn (1.00)
Ofloxacin R gyrA p.Asp94Asn (1.00)
Levofloxacin R gyrA p.Asp94Asn (1.00)
Ciprofloxacin R gyrA p.Asp94Asn (1.00)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
Cycloserine R alr p.Leu113Arg (1.00)
Ethionamide R fabG1 c.-17G>T (1.00), ethA p.Ala381Pro (1.00)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 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 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
fabG1 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
rpsA 1834840 p.Glu433Asp missense_variant 0.15 pyrazinamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288724 c.517dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
alr 3841083 p.Leu113Arg missense_variant 1.0 cycloserine
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
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
gyrA 9309 p.Asp670Tyr missense_variant 0.12
fgd1 491536 p.Leu252Met missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 762417 p.Arg871Ser missense_variant 0.11
rpoC 762794 c.-576C>G upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763873 c.504C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775798 c.2682_2683insCTG conservative_inframe_insertion 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777396 p.Ser362Thr missense_variant 0.17
mmpL5 777424 p.Leu353Met missense_variant 0.14
mmpL5 777763 c.718C>T synonymous_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781485 c.-75C>A upstream_gene_variant 0.12
fbiC 1303625 p.Gly232Asp missense_variant 0.12
Rv1258c 1407205 p.Ile46Val missense_variant 0.12
embR 1416522 p.Val276Leu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474669 n.1015delC non_coding_transcript_exon_variant 0.11
rrl 1475219 n.1562A>G non_coding_transcript_exon_variant 0.12
fabG1 1673879 p.Ile147Asn missense_variant 0.12
fabG1 1674002 p.Thr188Ile missense_variant 0.13
inhA 1674117 c.-85C>T upstream_gene_variant 0.14
inhA 1674484 p.Ile95Phe missense_variant 0.12
inhA 1674972 c.771C>T synonymous_variant 0.12
rpsA 1834000 c.459G>A synonymous_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834339 c.798C>T synonymous_variant 0.17
rpsA 1834436 p.Gly299Ser missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102072 p.Ala324Val missense_variant 0.11
katG 2154594 p.Glu506Asp missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170592 c.21G>A synonymous_variant 0.14
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289193 p.Gly17Cys missense_variant 0.17
kasA 2519157 p.Gly348Asp missense_variant 0.12
kasA 2519209 c.1095C>G synonymous_variant 0.18
folC 2746715 p.Gly295Val missense_variant 0.13
folC 2747065 c.534C>T synonymous_variant 0.15
pepQ 2859785 c.634C>T synonymous_variant 0.17
Rv2752c 3066032 p.Glu54Lys missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087895 c.1081dupG frameshift_variant 0.13
fbiD 3338919 c.-199C>A upstream_gene_variant 0.12
fbiD 3339384 c.267C>A synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474003 c.-4G>T upstream_gene_variant 0.12
fprA 3474916 p.Ala304Thr missense_variant 0.17
Rv3236c 3612169 p.Arg315Trp missense_variant 0.12
Rv3236c 3612438 c.679T>C synonymous_variant 0.15
Rv3236c 3612687 p.Gly144Ser missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641816 c.282C>A synonymous_variant 0.12
fbiB 3641861 c.327C>T synonymous_variant 0.13
alr 3840662 c.759G>A synonymous_variant 0.13
alr 3841264 p.Arg53Cys missense_variant 0.12
rpoA 3878180 p.Ile110Val missense_variant 0.1
embA 4242622 c.-611C>T upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242672 p.Pro937Gln missense_variant 0.13
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244866 p.Ala545Val missense_variant 0.12
embA 4245879 p.Asp883Asn missense_variant 0.12
embA 4246465 p.Val1078Ala missense_variant 0.13
embB 4246626 p.Phe38Ser missense_variant 0.12
embB 4246979 p.Gly156Ser missense_variant 0.2
embB 4248758 p.Leu749Met missense_variant 0.1
aftB 4267042 p.Arg599Ser missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267768 c.1069C>T synonymous_variant 0.14
aftB 4268023 c.814C>T synonymous_variant 0.2
aftB 4268025 p.Val271Ala missense_variant 0.2
ethA 4326439 c.1035C>T synonymous_variant 0.11
ethA 4327774 c.-301G>A upstream_gene_variant 0.15
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
gid 4408287 c.-85G>A upstream_gene_variant 0.11