TB-Profiler result

Run: ERR2513994
Summary

Run ID: ERR2513994

Sample name:

Date: 31-03-2023 20:02:55

Number of reads: 3486509

Percentage reads mapped: 99.55

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 764841 p.Ile491Thr missense_variant 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289040 p.Trp68Gly missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326087 c.1386delA frameshift_variant 0.98 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
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 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
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.12
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.12
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.18
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.18
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.17
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.17
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.17
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.25
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.19
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.29
rrl 1474264 n.607T>G non_coding_transcript_exon_variant 0.4
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.4
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.4
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.4
rrl 1474282 n.625G>A non_coding_transcript_exon_variant 0.4
rrl 1474288 n.631C>T non_coding_transcript_exon_variant 0.5
rrl 1474292 n.636_651delTCCTCTCCGGAGGAGG non_coding_transcript_exon_variant 0.5
rrl 1474310 n.653_654insTGG non_coding_transcript_exon_variant 0.5
rrl 1474326 n.669T>A non_coding_transcript_exon_variant 0.5
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.5
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 1.0
rrl 1474487 n.830G>T non_coding_transcript_exon_variant 0.4
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.4
rrl 1474497 n.840G>T non_coding_transcript_exon_variant 0.4
rrl 1474503 n.846G>A non_coding_transcript_exon_variant 0.4
rrl 1474506 n.849C>A non_coding_transcript_exon_variant 0.4
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.4
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.4
rrl 1474517 n.860C>G non_coding_transcript_exon_variant 0.4
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.4
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.4
rrl 1474774 n.1117A>G non_coding_transcript_exon_variant 0.4
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.25
rrl 1474800 n.1143T>C non_coding_transcript_exon_variant 0.25
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.25
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.25
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.25
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.25
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.25
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.2
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 2169927 p.Asn229Ser missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568795 c.-116A>G upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
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
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 0.99
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