TB-Profiler result

Run: ERR4799790
Summary

Run ID: ERR4799790

Sample name:

Date: 01-04-2023 09:22:24

Number of reads: 2560489

Percentage reads mapped: 99.55

Strain: lineage2.2.1

Drug-resistance: XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.98
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.98
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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 0.94 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.95 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.94 linezolid
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.86 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.93 isoniazid, ethionamide
katG 2155167 p.Ser315Thr missense_variant 0.97 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 0.98 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.96 ethambutol
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 575907 p.Ala187Val missense_variant 0.95
ccsA 620625 p.Ile245Met missense_variant 0.97
rpoB 760166 p.Asp120Glu missense_variant 0.12
rpoB 760202 p.Glu132Asp missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
rpoC 764817 p.Val483Gly missense_variant 0.88
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.92
mmpL5 776182 p.Asp767Asn missense_variant 0.83
mmpS5 778814 p.Phe31Ser missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.92
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472340 n.495C>T non_coding_transcript_exon_variant 0.4
rrs 1473033 n.1188A>G non_coding_transcript_exon_variant 0.22
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.5
rrl 1474629 n.972G>A non_coding_transcript_exon_variant 0.5
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.5
rrl 1474639 n.982G>T non_coding_transcript_exon_variant 0.5
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.4
rrl 1474710 n.1053T>A non_coding_transcript_exon_variant 0.33
rrl 1475951 n.2294G>A non_coding_transcript_exon_variant 0.88
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918472 p.Val178Ala missense_variant 0.97
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.94
PPE35 2169505 p.Gly370Ser missense_variant 0.12
Rv1979c 2223010 p.Val52Gly missense_variant 0.81
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288683 c.559T>G stop_lost&splice_region_variant 0.93
ribD 2986921 c.88delC frameshift_variant 0.97
thyA 3074268 c.203delA frameshift_variant 0.82
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.96
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327289 p.Leu62Pro missense_variant 0.77
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.95