TB-Profiler result

Run: ERR4423573
Summary

Run ID: ERR4423573

Sample name:

Date: 01-04-2023 05:53:59

Number of reads: 1061720

Percentage reads mapped: 99.7

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
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 1.0 rifampicin
rpoC 764948 p.Leu527Val missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
embB 4247429 p.Met306Val missense_variant 1.0 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
gyrB 5874 p.Arg212Met missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9632 c.2331C>A synonymous_variant 0.13
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
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763541 p.Trp58Arg missense_variant 0.14
rpoC 763555 c.186C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776366 c.2115G>T synonymous_variant 0.2
mmpL5 778010 p.Gln157His missense_variant 0.17
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
mmpR5 779357 p.Arg123Met missense_variant 0.12
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
atpE 1461283 p.Val80Ala missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473265 n.1420C>T non_coding_transcript_exon_variant 0.67
rrl 1473386 n.-272G>T upstream_gene_variant 0.4
rrl 1475208 n.1551C>T non_coding_transcript_exon_variant 0.5
fabG1 1674082 p.Ala215Ser missense_variant 0.18
inhA 1674569 p.Ser123Leu missense_variant 0.15
inhA 1674612 c.411C>A synonymous_variant 0.13
inhA 1674619 p.Pro140Thr 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
ahpC 2726625 p.Gln145* stop_gained 0.17
thyA 3074283 p.Leu63Phe missense_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
rpoA 3877786 p.Ala241Asp missense_variant 0.22
rpoA 3878398 p.Ser37* stop_gained 0.5
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
ethA 4327547 c.-74C>A upstream_gene_variant 0.17
whiB6 4338591 c.-70G>T upstream_gene_variant 0.13
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