TB-Profiler result

Run: ERR8025488
Summary

Run ID: ERR8025488

Sample name:

Date: 19-05-2023 17:04:33

Number of reads: 2859867

Percentage reads mapped: 99.64

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 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 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
gyrB 6083 p.Gly282Cys missense_variant 0.19
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7451 c.150C>A synonymous_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8872 p.Gly524Val missense_variant 0.15
gyrA 8919 p.Gly540Cys missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491603 p.Ala274Val missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619814 c.-77G>A upstream_gene_variant 0.14
rpoB 759746 c.-61C>A upstream_gene_variant 0.12
rpoB 761074 p.Glu423Gly missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763416 p.Thr16Ile missense_variant 0.18
rpoC 765608 c.2240delA frameshift_variant 0.15
rpoC 766595 p.Val1076Ile missense_variant 0.11
rpoC 766969 c.3600C>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775989 p.Leu831Pro missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776247 p.Ala745Asp missense_variant 0.18
mmpL5 776765 c.1716G>T synonymous_variant 0.13
mmpL5 777668 c.813C>A synonymous_variant 0.17
mmpS5 778866 c.38_39dupTC frameshift_variant 0.14
mmpL5 778885 c.-405T>C upstream_gene_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.13
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.22
rrl 1476002 n.2349_2350dupGT non_coding_transcript_exon_variant 0.29
fabG1 1674068 p.Arg210Leu missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834706 p.Asn389Asp missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102425 c.618G>A synonymous_variant 0.12
katG 2154100 p.Ser671Leu missense_variant 0.14
katG 2154212 p.Leu634Ile missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167930 c.2682delC frameshift_variant 0.13
PPE35 2167969 p.Pro882Thr missense_variant 0.12
PPE35 2168824 p.Pro597Ser missense_variant 0.13
PPE35 2168852 c.1761G>T synonymous_variant 0.13
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289603 c.-362G>T upstream_gene_variant 0.17
pncA 2289697 c.-456G>T upstream_gene_variant 0.15
kasA 2518549 c.435C>A synonymous_variant 0.12
eis 2714953 p.Gly127Asp missense_variant 0.12
Rv2752c 3065912 p.Leu94Ile missense_variant 0.14
Rv2752c 3066129 c.63G>T synonymous_variant 0.12
Rv2752c 3066136 p.Thr19Asn missense_variant 0.12
thyX 3067547 c.399C>A synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339471 c.354G>A synonymous_variant 0.12
Rv3083 3449053 p.Gly184Ser missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474280 p.Glu92* stop_gained 0.22
fprA 3474796 p.His264Tyr missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641124 c.-411C>T upstream_gene_variant 0.18
fbiB 3642689 c.1155G>T synonymous_variant 0.18
embC 4241792 p.Ser644Pro missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245072 c.1840C>T synonymous_variant 0.13
embA 4245981 p.Gly917* stop_gained 0.12
embA 4246003 p.Asn924Ser missense_variant 0.12
embB 4248611 p.Arg700Gly missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267659 p.Pro393Leu missense_variant 0.12
aftB 4268678 c.159G>A synonymous_variant 0.2
ubiA 4269339 c.494delG frameshift_variant 0.11
whiB6 4338512 p.Ala4Thr missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338645 c.-124G>A upstream_gene_variant 0.14
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.95