TB-Profiler result

Run: ERR8025536
Summary

Run ID: ERR8025536

Sample name:

Date: 18-05-2023 01:07:17

Number of reads: 2709372

Percentage reads mapped: 99.73

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
Rifampicin R rpoB p.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (1.00), katG c.826delC (0.25)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Val130Ala (1.00)
Streptomycin
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (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
Ethionamide R fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (1.00), ethR p.Ala95Thr (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
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
katG 2155285 c.826delC frameshift_variant 0.25 isoniazid
pncA 2288853 p.Val130Ala missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethR 4327831 p.Ala95Thr missense_variant 1.0 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
gyrB 5617 c.378G>T synonymous_variant 0.2
gyrB 5758 c.519C>T synonymous_variant 0.25
gyrA 6334 c.-968G>A upstream_gene_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8173 p.Val291Asp missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491126 p.Ala115Asp missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759738 c.-69G>T upstream_gene_variant 0.13
rpoB 760286 c.480C>T synonymous_variant 0.17
rpoB 761482 p.Ala559Val missense_variant 0.17
rpoB 761817 c.2011C>A synonymous_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 1.0
rpoC 763771 c.402C>T synonymous_variant 0.12
rpoC 763848 p.Lys160Met missense_variant 0.12
rpoC 765617 p.Glu750Gln missense_variant 1.0
rpoC 766456 c.3087C>A synonymous_variant 0.15
rpoC 766742 p.Gln1125* stop_gained 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777151 p.Asn444Tyr missense_variant 0.12
mmpL5 777256 p.Pro409Ser missense_variant 0.11
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
mmpR5 779363 p.Leu125Pro missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779627 c.-722T>C upstream_gene_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305103 c.2174delT frameshift_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474666 n.1012delG non_coding_transcript_exon_variant 0.4
rrl 1474911 n.1254G>T non_coding_transcript_exon_variant 0.2
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 1.0
rpsA 1833414 c.-127delT upstream_gene_variant 0.17
rpsA 1833847 c.306C>A synonymous_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834646 p.Tyr369His missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102980 c.63A>G synonymous_variant 0.11
katG 2153979 c.2133T>C synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155787 p.Ala109Thr missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168473 c.2139dupC frameshift_variant 0.2
PPE35 2168752 p.Ser621Gly missense_variant 0.12
Rv1979c 2222081 p.Ala362Thr missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289078 p.Gly55Asp missense_variant 0.12
ahpC 2726639 c.447C>G synonymous_variant 0.12
ahpC 2726758 p.Glu189Gly missense_variant 0.15
ribD 2986646 c.-193G>T upstream_gene_variant 0.13
ald 3086695 c.-125C>A upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449196 c.693C>T synonymous_variant 0.15
fprA 3473958 c.-49C>A upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474089 p.Thr28Met missense_variant 0.15
whiB7 3568699 c.-20G>T upstream_gene_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640878 c.-657T>C upstream_gene_variant 0.14
rpoA 3877521 c.987C>A synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243050 p.Leu1063Ser missense_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249696 p.Trp1061* stop_gained 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267743 p.Arg365Leu missense_variant 0.12
aftB 4269003 c.-167C>A upstream_gene_variant 0.12
ubiA 4269373 p.Ser154* stop_gained 0.13
ethA 4326187 c.1287G>A synonymous_variant 0.4
ethR 4327633 p.Ile29Phe missense_variant 0.18
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