TB-Profiler result

Run: ERR8025534
Summary

Run ID: ERR8025534

Sample name:

Date: 19-05-2023 17:31:26

Number of reads: 2671185

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 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 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
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
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 8014 p.Gln238Pro missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9410 p.Met703Ile missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619759 c.-132C>A upstream_gene_variant 0.13
rpoB 761961 p.Pro719Ser missense_variant 0.13
rpoB 762015 p.Glu737Lys missense_variant 0.15
rpoB 762493 c.2689delG frameshift_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764246 p.Leu293Ile missense_variant 0.13
rpoC 765485 p.Met706Leu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777751 p.Arg244Ser missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 0.95
mmpS5 779687 c.-782C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303287 c.357C>G synonymous_variant 0.11
embR 1416873 p.Val159Ile missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674193 c.-9A>G upstream_gene_variant 0.1
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834850 p.Ala437Thr missense_variant 0.12
tlyA 1917746 c.-193delA upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918245 c.306C>T synonymous_variant 0.14
ndh 2102391 p.Pro218Thr missense_variant 0.14
ndh 2102749 c.294C>T synonymous_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155730 p.Arg128Trp missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170306 p.Ala103Ser missense_variant 0.11
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518507 c.393G>T synonymous_variant 0.12
eis 2714766 c.567G>T synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448930 c.428delA frameshift_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474759 c.753G>T synonymous_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840568 p.Lys285Glu missense_variant 0.1
alr 3840636 p.Pro262Gln missense_variant 0.13
clpC1 4039941 p.Leu255Pro missense_variant 0.12
embC 4240672 c.810C>T synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245119 c.1887C>T synonymous_variant 0.17
embA 4245454 p.Ala741Asp missense_variant 0.18
embA 4245474 p.Gly748Ser missense_variant 0.22
embB 4249220 p.Ala903Thr missense_variant 0.14
aftB 4267512 p.Leu442His missense_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268505 p.Arg111Leu missense_variant 0.25
ubiA 4269245 p.His197Tyr missense_variant 0.13
ubiA 4269380 p.Val152Ile missense_variant 0.12
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