TB-Profiler result

Run: ERR108494
Summary

Run ID: ERR108494

Sample name:

Date: 31-03-2023 11:20:10

Number of reads: 4966939

Percentage reads mapped: 99.56

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 761110 p.Asp435Val missense_variant 0.85 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.2 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.17 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.81 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.78 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2288952 p.Gly97Asp missense_variant 0.2 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.74 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.16 kanamycin
embB 4247429 p.Met306Val missense_variant 0.8 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 8428 p.Arg376Leu missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
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 764918 p.Val517Leu missense_variant 0.18
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 779615 c.-710C>G upstream_gene_variant 0.99
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
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
PPE35 2169016 p.Thr533Ala missense_variant 0.72
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746747 c.852G>C synonymous_variant 0.75
ribD 2986827 c.-12G>A upstream_gene_variant 0.76
ribD 2987307 p.Ala157Pro missense_variant 0.2
thyA 3073806 c.666C>G synonymous_variant 0.23
ald 3086731 c.-89A>G upstream_gene_variant 0.18
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 4038857 c.1848C>A synonymous_variant 0.18
embC 4242425 p.Arg855Gly missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.17
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326083 p.Asp464Gly missense_variant 0.75
whiB6 4338371 p.Thr51Pro missense_variant 0.19
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