TB-Profiler result

Run: ERR4831910

Summary

Run ID: ERR4831910

Sample name:

Date: 01-04-2023 21:12:27

Number of reads: 1006663

Percentage reads mapped: 99.22

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 0.98
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.Ser450Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289054 p.Asp63Gly missense_variant 0.27 pyrazinamide
pncA 2289228 p.Ile5Thr missense_variant 0.41 pyrazinamide
folC 2747328 p.Arg91Trp missense_variant 0.17 para-aminosalicylic_acid
ddn 3986989 p.Leu49Pro missense_variant 1.0 delamanid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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
mmpL5 776471 p.Gln670His missense_variant 0.13
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 1417089 p.Gly87Arg missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.26
fabG1 1673359 c.-81T>C upstream_gene_variant 0.26
fabG1 1673361 c.-79C>G upstream_gene_variant 0.26
fabG1 1673380 c.-60C>G upstream_gene_variant 0.28
rpsA 1833392 c.-150C>A upstream_gene_variant 0.14
rpsA 1834098 p.Ser186Phe missense_variant 0.11
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
katG 2155690 p.Leu141Ser missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169717 p.Asn299Ile missense_variant 0.17
PPE35 2169719 c.894C>T synonymous_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.45
PPE35 2170053 p.Thr187Ser missense_variant 0.45
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.15
embB 4246555 c.42G>C synonymous_variant 0.14
embB 4246556 p.Ala15Pro missense_variant 0.14
embB 4247106 p.Pro198Arg missense_variant 0.1
embB 4248115 c.1602C>T synonymous_variant 1.0
aftB 4267114 c.1721_1722delTG frameshift_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268184 p.Gly218Val missense_variant 0.11
ubiA 4269133 p.Gly234Val missense_variant 1.0
ubiA 4269155 p.Thr227Ala missense_variant 0.1
ethA 4328378 c.-905G>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338599 c.-78A>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0