TB-Profiler result

Run: ERR2516727

Summary

Run ID: ERR2516727

Sample name:

Date: 31-03-2023 21:41:58

Number of reads: 963503

Percentage reads mapped: 99.59

Strain: lineage2.2.1.1

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
ahpC 2726141 c.-52C>T upstream_gene_variant 0.19 isoniazid
ahpC 2726145 c.-48G>A upstream_gene_variant 0.22 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326213 p.Arg421* stop_gained 0.14 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 490865 p.Glu28Gly missense_variant 0.11
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 760983 p.Val393Met missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775939 p.Ala848Ser missense_variant 0.11
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777999 p.Leu161Pro missense_variant 0.13
mmpL5 778923 c.-443C>T upstream_gene_variant 0.17
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 1471864 n.19A>G non_coding_transcript_exon_variant 0.12
fabG1 1673512 c.78dupG frameshift_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102693 p.Val117Ala missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154857 p.Asp419Tyr missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168561 c.2052T>C synonymous_variant 0.1
PPE35 2168772 p.Leu614Ser missense_variant 0.12
Rv1979c 2221743 c.1422T>C synonymous_variant 0.1
Rv1979c 2222912 p.Ala85Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288772 p.Val157Ala missense_variant 0.23
pncA 2288959 p.Tyr95Asp missense_variant 1.0
pncA 2289098 c.144G>A synonymous_variant 0.12
eis 2714447 c.886T>C synonymous_variant 0.12
eis 2714846 p.Val163Ile missense_variant 1.0
ahpC 2726775 p.Ala195Ser missense_variant 0.11
pepQ 2860502 c.-84A>G upstream_gene_variant 0.11
ribD 2986894 p.Ser19Leu missense_variant 0.12
ribD 2987473 p.Cys212Tyr missense_variant 0.14
thyA 3073840 p.Asn211Ser missense_variant 0.12
ald 3086745 c.-75G>A upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339127 p.Thr4Pro missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3877960 p.Val183Gly missense_variant 1.0
clpC1 4038702 p.Leu668Pro missense_variant 0.11
clpC1 4040501 c.204C>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244992 p.Val587Ala missense_variant 0.11
embB 4248115 c.1602C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4269810 c.-974A>G upstream_gene_variant 0.22
ethA 4327065 p.Cys137Arg missense_variant 0.36
ethR 4327976 p.Gln143Arg missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>C upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0