TB-Profiler result

Run: ERR11489020
Summary

Run ID: ERR11489020

Sample name:

Date: 07-01-2024 03:00:49

Number of reads: 3770037

Percentage reads mapped: 97.4

Strain: lineage2.2.1

Drug-resistance: MDR-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 (0.97)
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol R embB p.Met306Val (0.98)
Pyrazinamide
Streptomycin R rrs n.462C>T (0.21)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (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 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
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.21 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
embB 4247429 p.Met306Val missense_variant 0.98 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.98
gyrA 9304 p.Gly668Asp missense_variant 0.98
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 760283 c.477G>C synonymous_variant 0.17
rpoB 760298 c.492G>C synonymous_variant 0.19
rpoB 760310 c.504G>C synonymous_variant 0.2
rpoB 760328 c.522G>C synonymous_variant 0.23
rpoB 760331 c.525G>C synonymous_variant 0.22
rpoB 760340 c.534G>T synonymous_variant 0.22
rpoB 760361 c.555T>C synonymous_variant 0.2
rpoB 760376 p.Asp190Glu missense_variant 0.19
rpoB 760380 p.Thr192Leu missense_variant 0.18
rpoB 760406 c.600G>C synonymous_variant 0.15
rpoB 760412 c.606C>G synonymous_variant 0.14
rpoB 761314 p.Phe503Ser missense_variant 0.96
rpoB 761891 c.2085G>C synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 0.92
rpoC 763594 c.225C>T synonymous_variant 0.12
rpoC 763648 c.279C>T synonymous_variant 0.13
rpoC 763660 c.291T>G synonymous_variant 0.15
rpoC 763666 c.297G>T synonymous_variant 0.16
rpoC 763675 c.306C>G synonymous_variant 0.16
rpoC 763696 c.327T>C synonymous_variant 0.17
rpoC 763702 c.333C>G synonymous_variant 0.17
rpoC 763717 c.348T>C synonymous_variant 0.16
rpoC 763723 c.354G>C synonymous_variant 0.14
rpoC 763732 c.363C>G synonymous_variant 0.13
rpoC 763735 c.366G>C synonymous_variant 0.12
rpoC 763741 c.372C>T synonymous_variant 0.13
rpoC 763744 c.375G>C synonymous_variant 0.13
rpoC 764257 c.888G>C synonymous_variant 0.13
rpoC 764266 c.897T>C synonymous_variant 0.12
rpoC 764269 c.900G>C synonymous_variant 0.12
rpoC 764278 c.909A>G synonymous_variant 0.13
rpoC 764858 c.1489T>C synonymous_variant 0.13
rpoC 764872 c.1503A>G synonymous_variant 0.14
rpoC 764911 c.1542A>G synonymous_variant 0.12
rpoC 766945 c.3576A>C synonymous_variant 0.12
rpoC 766978 c.3609C>G synonymous_variant 0.13
rpoC 766996 c.3627C>T synonymous_variant 0.15
rpoC 767035 c.3666G>C synonymous_variant 0.17
rpoC 767059 c.3690T>G synonymous_variant 0.19
rpoC 767062 c.3693C>A synonymous_variant 0.19
rpoC 767098 c.3729T>C synonymous_variant 0.16
rpoC 767119 c.3750A>G synonymous_variant 0.16
rpoC 767134 c.3765C>A synonymous_variant 0.16
rpoC 767180 p.Ala1271Gln missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.17
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.17
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.16
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.12
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.15
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.18
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.15
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.16
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.15
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.16
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.17
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.12
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.12
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.18
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.18
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.17
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.17
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.17
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.17
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.17
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.17
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.14
rrl 1476732 n.3075T>C non_coding_transcript_exon_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154113 p.Thr667Pro missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518588 c.474T>G synonymous_variant 0.12
kasA 2518591 c.477G>C synonymous_variant 0.12
kasA 2518678 c.564C>T synonymous_variant 0.13
kasA 2518687 c.573C>T synonymous_variant 0.12
kasA 2518705 c.591T>G synonymous_variant 0.13
kasA 2518711 c.597A>G synonymous_variant 0.13
kasA 2518714 c.600A>T synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4038812 c.1893T>C synonymous_variant 0.15
clpC1 4038815 c.1890G>C synonymous_variant 0.16
clpC1 4038878 c.1827A>G synonymous_variant 0.19
clpC1 4038908 c.1797C>G synonymous_variant 0.23
clpC1 4038914 c.1791G>C synonymous_variant 0.23
clpC1 4038923 c.1780_1782delCTAinsTTG synonymous_variant 0.22
clpC1 4038953 c.1752A>G synonymous_variant 0.23
clpC1 4038965 c.1740T>C synonymous_variant 0.18
clpC1 4038971 c.1734T>C synonymous_variant 0.14
clpC1 4038974 c.1731T>C synonymous_variant 0.15
clpC1 4038989 c.1716T>C synonymous_variant 0.16
clpC1 4038997 c.1708T>C synonymous_variant 0.15
clpC1 4039010 c.1695G>A synonymous_variant 0.15
clpC1 4039022 c.1683A>G synonymous_variant 0.14
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
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