TB-Profiler result

Run: ERR4832050
Summary

Run ID: ERR4832050

Sample name:

Date: 01-04-2023 21:17:40

Number of reads: 484237

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 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 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289043 p.Ser67Pro missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4248003 p.Gln497Pro 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 491127 c.345C>G synonymous_variant 0.14
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 761330 c.1524G>T synonymous_variant 0.14
rpoB 761690 c.1884G>A synonymous_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764354 p.Gln329Lys 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
mmpR5 778993 p.Ser2Cys missense_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304159 p.Val410Gly missense_variant 0.5
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
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 2170048 p.Leu189Val missense_variant 0.76
PPE35 2170053 p.Thr187Ser missense_variant 0.72
Rv1979c 2222503 p.Met221Thr missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289049 p.Ser65Pro missense_variant 0.2
eis 2714846 p.Val163Ile missense_variant 1.0
pepQ 2859454 p.Val322Gly missense_variant 0.29
ribD 2987143 p.Gln102Arg missense_variant 0.12
thyX 3067443 p.Arg168Leu missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612018 p.Pro367Thr missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640374 c.-169A>G upstream_gene_variant 1.0
alr 3841506 c.-86A>C upstream_gene_variant 0.18
panD 4044312 c.-31G>A upstream_gene_variant 0.15
embC 4240176 p.Leu105Ser missense_variant 0.12
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 0.17
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.2
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4249797 p.Arg1095Gln missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326540 p.Val312Leu missense_variant 0.13
whiB6 4338365 p.Cys53Gly missense_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