TB-Profiler result

Run: ERR8025625
Summary

Run ID: ERR8025625

Sample name:

Date: 20-05-2023 19:13:01

Number of reads: 2958515

Percentage reads mapped: 99.58

Strain: lineage2.2.2;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
Rifampicin R rpoB p.Asp435Val (1.00)
Isoniazid R fabG1 c.-17G>T (0.93), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA c.517dupG (0.74), pncA c.517dupG (0.74), pncA p.Thr160Ala (0.17), pncA p.Thr100Ile (0.13)
Streptomycin R rrs n.514A>C (1.00), gid p.Leu79Ser (0.79)
Fluoroquinolones R gyrA p.Ala90Val (0.35), gyrA p.Asp94Asn (0.67)
Moxifloxacin R gyrA p.Ala90Val (0.35), gyrA p.Asp94Asn (0.67)
Ofloxacin R gyrA p.Ala90Val (0.35), gyrA p.Asp94Asn (0.67)
Levofloxacin R gyrA p.Ala90Val (0.35), gyrA p.Asp94Asn (0.67)
Ciprofloxacin R gyrA p.Ala90Val (0.35), gyrA p.Asp94Asn (0.67)
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 (0.91)
Ethionamide R fabG1 c.-17G>T (0.93), ethA p.Ala381Pro (0.75), ethA p.Gly43Cys (0.18)
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
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.17
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.85
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 0.35 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Asn missense_variant 0.67 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 0.93 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288724 c.517dupG frameshift_variant 0.74 pyrazinamide, pyrazinamide
pncA 2288764 p.Thr160Ala missense_variant 0.17 pyrazinamide
pncA 2288943 p.Thr100Ile missense_variant 0.13 pyrazinamide
alr 3841083 p.Leu113Arg missense_variant 0.91 cycloserine
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 0.75 ethionamide
ethA 4327347 p.Gly43Cys missense_variant 0.18 ethionamide
gid 4407967 p.Leu79Ser missense_variant 0.79 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
fgd1 491328 c.546C>G synonymous_variant 0.15
fgd1 491330 p.Lys183Met missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.32
ccsA 619895 p.Asn2Ser missense_variant 0.1
ccsA 620625 p.Ile245Met missense_variant 0.23
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764822 p.Asp485Tyr missense_variant 0.19
rpoC 766818 p.His1150Pro missense_variant 0.18
mmpL5 775592 c.2889G>A synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.2
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 0.42
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674468 c.271dupG frameshift_variant 0.11
inhA 1674868 p.Asp223Asn missense_variant 0.1
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918043 p.Asp35Ala missense_variant 0.17
tlyA 1918179 c.240G>A synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221939 p.Arg409Gln missense_variant 0.68
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746844 p.Ala252Val missense_variant 0.11
folC 2746878 c.718_720delAAG conservative_inframe_deletion 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449315 p.Trp271* stop_gained 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475175 p.Lys390Met missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4039410 p.Arg432Pro missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249160 p.Ile883Phe missense_variant 0.12
embB 4249248 p.Pro912Leu missense_variant 0.15
embB 4249605 p.Gly1031Asp missense_variant 0.11
aftB 4267310 c.1527G>A synonymous_variant 0.15
aftB 4267539 p.Pro433Gln missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268623 p.Trp72Arg missense_variant 0.13
ubiA 4269992 c.-159C>T upstream_gene_variant 0.12
whiB6 4338365 p.Cys53Arg missense_variant 0.3
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