TB-Profiler result

Run: ERR4827464
Summary

Run ID: ERR4827464

Sample name:

Date: 01-04-2023 18:04:21

Number of reads: 973699

Percentage reads mapped: 99.27

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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289072 p.His57Arg missense_variant 1.0 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 0.71 kanamycin
embA 4243221 c.-12C>T upstream_gene_variant 0.16 ethambutol
embB 4247429 p.Met306Val 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 619738 c.-153T>C upstream_gene_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764669 p.Pro434Thr missense_variant 0.96
rpoC 766645 p.Glu1092Asp 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 777076 c.1402_1404delATC conservative_inframe_deletion 0.12
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
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.12
Rv1258c 1406946 p.Ala132Gly missense_variant 0.12
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
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 2155191 c.921A>C synonymous_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.63
PPE35 2170053 p.Thr187Ser missense_variant 0.62
Rv1979c 2223087 c.78G>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746318 c.1281C>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474609 c.603T>C synonymous_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642383 c.849C>A synonymous_variant 0.13
alr 3841403 p.Glu6Asp missense_variant 1.0
rpoA 3877756 p.Ile251Thr missense_variant 0.1
embC 4240133 p.Ala91Thr missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.3
embB 4246555 c.42G>C synonymous_variant 0.35
embB 4246556 p.Ala15Pro missense_variant 0.35
embB 4246563 p.Leu17Trp missense_variant 0.23
embB 4246567 c.54G>T synonymous_variant 0.23
embB 4246584 p.Arg24Pro missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 0.93
whiB6 4338563 c.-42G>T upstream_gene_variant 1.0
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