TB-Profiler result

Run: ERR5863904
Summary

Run ID: ERR5863904

Sample name:

Date: 01-04-2023 22:58:58

Number of reads: 547130

Percentage reads mapped: 99.46

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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289009 p.Gly78Asp missense_variant 1.0 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
ethA 4326770 c.703delT frameshift_variant 1.0 ethionamide, 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 8055 p.Arg252* stop_gained 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491582 p.Glu267Gly missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575981 c.634C>A synonymous_variant 0.5
rpoB 760014 p.Glu70* stop_gained 0.29
rpoB 761832 p.Thr676Ala missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766080 p.Arg904His missense_variant 0.33
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 779373 c.-893G>T upstream_gene_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302947 p.Gly6Val missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461015 c.-30G>T upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472804 n.960delC non_coding_transcript_exon_variant 0.4
rrl 1476097 n.2440C>A non_coding_transcript_exon_variant 0.33
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 2169463 p.Val384Ile missense_variant 0.14
PPE35 2170413 p.Ala67Glu missense_variant 0.29
Rv1979c 2223167 c.-4delT upstream_gene_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519027 p.Ile305Val missense_variant 0.33
eis 2715329 p.Thr2Ser missense_variant 0.13
ahpC 2726134 c.-59C>A upstream_gene_variant 0.11
folC 2746180 c.1414_1418dupGTTGT frameshift_variant 0.2
pepQ 2859306 c.1113T>C synonymous_variant 0.17
ribD 2987474 c.636T>C synonymous_variant 0.22
Rv2752c 3065686 p.Gly169Val missense_variant 0.29
thyA 3074283 c.188delT frameshift_variant 0.17
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338963 c.-155C>A upstream_gene_variant 0.13
Rv3083 3449704 p.Ile401Phe missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613095 c.22T>C synonymous_variant 0.4
alr 3841263 p.Arg53His missense_variant 0.12
clpC1 4039359 p.Ser449Ile missense_variant 0.18
embC 4239747 c.-116A>G upstream_gene_variant 0.17
embC 4239810 c.-53G>T upstream_gene_variant 0.18
embC 4240980 p.Thr373Lys missense_variant 0.15
embC 4241707 c.1845G>T synonymous_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242679 c.-554C>A upstream_gene_variant 0.33
embC 4242996 c.3136dupG frameshift_variant 0.18
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245284 c.2052C>A synonymous_variant 0.2
aftB 4267369 c.1467dupC frameshift_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268781 p.Trp19Leu missense_variant 0.5
ethR 4327595 p.Arg16His missense_variant 0.29
whiB6 4338371 p.Thr51Pro 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