TB-Profiler result

Run: ERR4831759
Summary

Run ID: ERR4831759

Sample name:

Date: 01-04-2023 21:06:09

Number of reads: 885641

Percentage reads mapped: 99.16

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 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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 761139 p.His445Tyr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Asp missense_variant 1.0 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 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776095 p.Arg796Ser missense_variant 0.13
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304343 c.1413T>G synonymous_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472890 n.1045C>A non_coding_transcript_exon_variant 0.12
rrs 1473268 n.1423C>A non_coding_transcript_exon_variant 0.17
rrl 1473501 n.-157C>T upstream_gene_variant 0.11
rrl 1474738 n.1081G>T non_coding_transcript_exon_variant 0.18
rrl 1475603 n.1946G>T non_coding_transcript_exon_variant 0.13
rrl 1476048 n.2391G>T non_coding_transcript_exon_variant 0.17
fabG1 1673882 p.Gly148Ala missense_variant 0.12
rpsA 1833703 c.162C>T synonymous_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102787 c.256T>C synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167912 p.Ala901Ser missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168618 c.1995G>A synonymous_variant 0.14
PPE35 2168814 p.Thr600Asn missense_variant 0.15
PPE35 2169519 p.Gly365Val missense_variant 0.17
PPE35 2169558 p.Phe352Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517953 c.-162C>T upstream_gene_variant 0.11
ahpC 2726338 p.Val49Gly missense_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475267 p.Ala421Thr missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613167 c.-51C>T upstream_gene_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249514 p.Leu1001Val missense_variant 0.1
aftB 4266952 c.1884delA frameshift_variant&stop_lost&splice_region_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338189 c.333G>T synonymous_variant 0.11
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