TB-Profiler result

Run: ERR5866419
Summary

Run ID: ERR5866419

Sample name:

Date: 02-04-2023 00:40:34

Number of reads: 1287003

Percentage reads mapped: 98.17

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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Glu missense_variant 1.0 pyrazinamide
embB 4247399 p.Asn296His missense_variant 1.0 ethambutol
ethA 4327363 c.110delA frameshift_variant 1.0 ethionamide, 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 7164 p.Ala642Asp missense_variant 0.13
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 9578 c.2277C>T synonymous_variant 0.12
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 760544 p.Phe246Leu missense_variant 0.12
rpoB 762226 p.Glu807Gly missense_variant 0.74
rpoB 762798 p.Ala998Thr missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764573 p.Leu402Phe missense_variant 1.0
rpoC 765678 p.Arg770His missense_variant 1.0
rpoC 766730 p.Val1121Leu missense_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776087 c.2394C>T synonymous_variant 0.17
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776294 p.Gln729His missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781745 c.186G>A synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.2
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 0.11
rrl 1474352 n.695G>A non_coding_transcript_exon_variant 0.11
rrl 1475382 n.1725A>C non_coding_transcript_exon_variant 0.5
fabG1 1673476 p.Phe13Ile missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102848 p.Glu65Asp missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222459 p.Glu236Lys missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290048 c.-807C>A upstream_gene_variant 0.11
kasA 2517973 c.-142G>A upstream_gene_variant 0.1
folC 2746982 p.Gly206Asp missense_variant 0.14
pepQ 2859531 c.887delA frameshift_variant 0.12
ribD 2986753 c.-86T>C upstream_gene_variant 0.11
Rv2752c 3065029 c.1162delG frameshift_variant 0.11
Rv2752c 3065760 c.431delT frameshift_variant 0.12
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339380 p.Asp88Gly missense_variant 0.22
Rv3083 3449510 p.Glu336Gly missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641662 p.Gly43Asp missense_variant 0.11
clpC1 4039109 p.Ile532Met missense_variant 0.1
clpC1 4039999 p.Gly236Ser missense_variant 0.11
embC 4239943 c.81G>T synonymous_variant 0.11
embC 4240815 p.Gly318Asp missense_variant 0.1
embC 4241726 p.Phe622Leu missense_variant 0.14
embC 4241747 p.Val629Met missense_variant 0.12
embC 4242225 p.Asn788Ser missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248051 p.Gly513Val missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268776 c.60delG frameshift_variant 0.11
whiB6 4338371 p.Thr51Pro 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