TB-Profiler result

Run: ERR8025681
Summary

Run ID: ERR8025681

Sample name:

Date: 18-05-2023 05:45:02

Number of reads: 2760727

Percentage reads mapped: 99.52

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 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 gyrB p.Glu501Asp (0.98)
Moxifloxacin R gyrB p.Glu501Asp (0.98)
Ofloxacin R gyrB p.Glu501Asp (0.98)
Levofloxacin R gyrB p.Glu501Asp (0.98)
Ciprofloxacin R gyrB p.Glu501Asp (0.98)
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
gyrB 6742 p.Glu501Asp missense_variant 0.98 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
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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575643 p.Pro99Leu missense_variant 0.25
ccsA 619881 c.-10G>T upstream_gene_variant 0.14
ccsA 620662 p.Tyr258His missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766783 c.3414C>T synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777629 c.851delG frameshift_variant 0.1
mmpR5 779240 p.Ala84Val missense_variant 0.29
mmpR5 779454 c.466dupC frameshift_variant 0.21
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304931 c.2001C>A synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917819 c.-121C>A upstream_gene_variant 0.14
tlyA 1917952 p.Ala5Thr missense_variant 0.12
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 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715090 c.242delG frameshift_variant 0.13
Rv2752c 3064658 p.Glu512* stop_gained 0.12
thyX 3067949 c.-4C>T upstream_gene_variant 1.0
thyA 3073799 p.Arg225Trp missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087080 c.261C>T synonymous_variant 0.11
Rv3083 3449765 p.Ala421Val missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474224 c.223delC frameshift_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640811 c.271delG frameshift_variant 0.12
fbiB 3642370 p.Ala279Val missense_variant 0.12
ddn 3986950 p.Gly36Asp missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242965 p.Ile1035Val missense_variant 0.11
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245366 p.Arg712Ser missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267963 p.Pro292Ala missense_variant 0.11
ubiA 4270009 c.-176C>T upstream_gene_variant 0.11
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