TB-Profiler result

Run: ERR5866524
Summary

Run ID: ERR5866524

Sample name:

Date: 02-04-2023 00:44:33

Number of reads: 924291

Percentage reads mapped: 99.48

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
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326231 c.1242delT 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
gyrB 5546 p.Leu103Ile missense_variant 0.14
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 490630 c.-153G>T upstream_gene_variant 0.25
fgd1 491264 p.Ser161* stop_gained 0.17
fgd1 491687 p.Thr302Ile missense_variant 0.29
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 759963 p.Asp53Tyr missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763503 p.Gly45Val missense_variant 0.15
rpoC 764822 p.Asp485Tyr missense_variant 1.0
rpoC 766209 p.Pro947Gln missense_variant 0.15
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766885 c.3516G>T synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776162 c.2319C>A synonymous_variant 0.2
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 778412 p.Phe23Leu missense_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800898 p.Lys30Asn missense_variant 0.4
rplC 801340 p.Leu178Ile missense_variant 0.18
fbiC 1303383 c.453G>T synonymous_variant 0.2
fbiC 1303758 c.828G>T synonymous_variant 0.2
Rv1258c 1406390 c.950delT frameshift_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674904 p.Ala235Ser missense_variant 0.17
rpsA 1834086 c.546_549delCGTG frameshift_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101875 p.Phe390Leu missense_variant 0.11
ndh 2103117 c.-75G>T upstream_gene_variant 0.29
katG 2154650 p.Lys488Glu missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156012 p.Gly34* stop_gained 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170707 c.-95G>T upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290011 c.-770C>A upstream_gene_variant 0.18
kasA 2518738 c.624G>T synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449190 c.687C>A synonymous_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568753 c.-74G>A upstream_gene_variant 0.33
Rv3236c 3612062 p.Ala352Asp missense_variant 0.14
Rv3236c 3612523 c.594G>A synonymous_variant 0.17
Rv3236c 3612591 p.Gly176Cys missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642715 p.Gly394Val missense_variant 0.14
alr 3840337 p.Glu362* stop_gained 0.25
rpoA 3877947 c.561C>A synonymous_variant 0.33
rpoA 3878015 p.Asp165Tyr missense_variant 0.22
rpoA 3878051 c.457C>A synonymous_variant 0.17
ddn 3986807 c.-37G>T upstream_gene_variant 0.15
clpC1 4040350 p.Val119Met missense_variant 0.18
embC 4239746 c.-117C>A upstream_gene_variant 0.2
embC 4240765 c.903C>A synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249193 p.Pro894Thr missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268400 p.Ala146Asp missense_variant 0.18
aftB 4269348 c.-512C>A upstream_gene_variant 0.17
ethA 4327863 c.-390G>A upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407733 p.Gly157Val missense_variant 0.22
gid 4407780 c.423G>T synonymous_variant 0.18
gid 4407927 p.Glu92Asp missense_variant 1.0