TB-Profiler result

Run: ERR4831725
Summary

Run ID: ERR4831725

Sample name:

Date: 01-04-2023 21:05:10

Number of reads: 606961

Percentage reads mapped: 99.47

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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Val missense_variant 1.0 pyrazinamide
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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.23
rpoB 760922 c.1116G>C synonymous_variant 0.12
rpoB 761042 c.1236C>A synonymous_variant 0.11
rpoB 761113 p.Gln436Arg missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764407 c.1038G>A synonymous_variant 0.2
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 778181 c.-809C>T upstream_gene_variant 0.17
mmpL5 778908 c.-428G>A upstream_gene_variant 0.11
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
atpE 1461275 c.231T>C synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472255 n.410A>G non_coding_transcript_exon_variant 0.13
rrs 1472298 n.453G>A non_coding_transcript_exon_variant 0.14
rrl 1474260 n.603A>G non_coding_transcript_exon_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102407 c.636T>A synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170053 p.Thr187Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 1.0
ribD 2987233 p.Val132Ala missense_variant 0.1
Rv2752c 3064797 c.1395G>T synonymous_variant 0.12
Rv2752c 3065634 c.558G>T synonymous_variant 0.11
thyA 3074648 c.-177T>G upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 p.Gln89* stop_gained 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641090 p.His183Arg missense_variant 0.14
alr 3841588 c.-168C>A upstream_gene_variant 0.11
ddn 3986712 c.-132A>C upstream_gene_variant 0.33
clpC1 4039480 p.Arg409Gly missense_variant 0.14
embC 4240846 c.984C>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 4244184 p.Ser318Leu missense_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.16
embB 4246695 p.Arg61Gln missense_variant 0.15
embB 4246903 c.390G>A synonymous_variant 1.0
embB 4247044 c.531C>A synonymous_variant 0.12
embB 4248115 c.1602C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4326598 c.-951T>C upstream_gene_variant 1.0
ethA 4328246 c.-773C>T upstream_gene_variant 0.11
ethA 4328413 c.-940C>A upstream_gene_variant 0.12
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