TB-Profiler result

Run: ERR8025522

Summary

Run ID: ERR8025522

Sample name:

Date: 18-05-2023 00:30:23

Number of reads: 2592549

Percentage reads mapped: 99.67

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.Ala379Val (0.12), 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 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.-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 7582 p.Asp94Gly 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
katG 2154976 p.Ala379Val missense_variant 0.12 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288724 c.517dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
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 7498 p.Pro66Gln missense_variant 0.25
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7709 c.410delT frameshift_variant 0.13
gyrA 7820 c.519G>A synonymous_variant 0.12
gyrA 7857 c.557delC frameshift_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491368 c.588delC frameshift_variant 0.17
fgd1 491432 p.Ala217Val missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760247 c.441C>T synonymous_variant 0.2
rpoB 760254 p.Asp150Asn missense_variant 0.2
rpoB 760337 c.531C>G synonymous_variant 0.25
rpoB 762135 p.Asp777Asn missense_variant 1.0
rpoC 762659 c.-711C>A upstream_gene_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763058 c.-312C>A upstream_gene_variant 0.15
rpoC 763856 p.Glu163* stop_gained 0.14
rpoC 763867 c.498C>A synonymous_variant 0.13
mmpL5 775622 c.2859C>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776071 p.Ile804Val missense_variant 0.14
mmpL5 776091 p.Ser797Ile missense_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778148 p.Gln111His missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800668 c.-141C>A upstream_gene_variant 0.13
rplC 800813 p.Ala2Glu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473755 n.98C>A non_coding_transcript_exon_variant 0.17
rrl 1473786 n.129C>A non_coding_transcript_exon_variant 0.13
rrl 1476234 n.2577G>A non_coding_transcript_exon_variant 0.2
rrl 1476337 n.2680C>A non_coding_transcript_exon_variant 0.25
rrl 1476608 n.2951C>T non_coding_transcript_exon_variant 0.2
fabG1 1673834 p.Phe132Ser missense_variant 0.11
fabG1 1674034 p.Gln199Lys missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
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
PPE35 2168198 c.2415G>A synonymous_variant 0.2
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2222777 p.Ala130Ser missense_variant 0.12
Rv1979c 2222993 p.Ala58Thr missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517918 c.-197C>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612027 p.Ile364Val missense_variant 0.12
Rv3236c 3612120 c.997C>A synonymous_variant 0.14
Rv3236c 3612344 p.Arg258Leu missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642217 p.Thr228Ile missense_variant 0.13
clpC1 4038223 p.Ala828Thr missense_variant 0.12
clpC1 4039205 c.1500C>A synonymous_variant 0.13
embA 4242637 c.-596C>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268899 c.-63G>T upstream_gene_variant 0.12
ubiA 4269892 c.-59G>T upstream_gene_variant 0.17
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