TB-Profiler result

Run: ERR5866471

Summary

Run ID: ERR5866471

Sample name:

Date: 02-04-2023 00:42:18

Number of reads: 418669

Percentage reads mapped: 99.09

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 1473247 n.1402C>T non_coding_transcript_exon_variant 0.89 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
ethA 4326166 c.1307dupC 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 5354 p.Glu39* stop_gained 0.15
gyrB 5981 p.Ser248Gly missense_variant 0.18
gyrB 7076 p.Leu613Ile missense_variant 0.14
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 491677 p.Gln299Lys missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620052 c.162G>T synonymous_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762250 p.Leu815Pro missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764916 p.Leu516Pro missense_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 777859 p.Glu208Lys missense_variant 0.25
mmpR5 779041 p.Glu18* stop_gained 0.15
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
embR 1416712 c.636C>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673880 c.-322C>A upstream_gene_variant 0.18
inhA 1674315 c.114C>A synonymous_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153999 c.2113C>A synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155394 p.Asp240Tyr missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169247 p.Thr456Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726081 c.-112C>G upstream_gene_variant 0.12
ahpC 2726226 p.Ala12Ser missense_variant 0.2
folC 2747230 c.369C>T synonymous_variant 0.2
pepQ 2859749 p.Ala224Ser missense_variant 0.14
pepQ 2859806 p.His205Asn missense_variant 0.17
pepQ 2860103 p.Gly106Cys missense_variant 0.12
Rv2752c 3065619 c.573C>A synonymous_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087095 p.Phe92Leu missense_variant 0.18
fbiD 3339529 p.Ser138Gly missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4239951 p.Arg30Leu missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244779 p.Ser516Tyr missense_variant 0.13
embA 4245786 p.Ala852Ser missense_variant 0.17
embB 4247308 p.Met265Ile missense_variant 0.15
embB 4248667 p.Phe718Leu missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268162 p.Gln225His missense_variant 0.25
ethA 4327174 p.Phe100Leu missense_variant 0.25
ethA 4328425 c.-952C>A upstream_gene_variant 0.3
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