TB-Profiler result

Run: ERR4819090
Summary

Run ID: ERR4819090

Sample name:

Date: 01-04-2023 15:55:08

Number of reads: 372093

Percentage reads mapped: 99.45

Strain: lineage2.2.1

Drug-resistance: HR-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 0.98
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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4248003 p.Gln497Arg 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
gyrB 5895 p.Val219Gly missense_variant 0.17
gyrB 6280 c.1041T>C synonymous_variant 0.2
gyrB 6286 c.1047T>C synonymous_variant 0.17
gyrB 6289 c.1050C>T synonymous_variant 0.18
gyrB 6292 c.1053G>C synonymous_variant 0.18
gyrA 6304 c.-998C>G upstream_gene_variant 0.2
gyrA 6307 c.-995T>G upstream_gene_variant 0.2
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 620069 p.Thr60Ser missense_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761628 p.Gln608* stop_gained 0.25
rpoB 762167 c.2361T>C synonymous_variant 0.22
rpoB 762170 c.2364C>G synonymous_variant 0.22
rpoB 762179 c.2373C>T synonymous_variant 0.29
rpoB 762185 c.2379G>C synonymous_variant 0.29
rpoB 762212 c.2406G>C synonymous_variant 0.33
rpoB 762233 c.2427G>C synonymous_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765946 c.2577C>T synonymous_variant 0.15
rpoC 765961 c.2592G>A synonymous_variant 0.18
rpoC 765962 c.2593T>C synonymous_variant 0.18
rpoC 765967 c.2598C>G synonymous_variant 0.2
rpoC 765994 c.2625A>T synonymous_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
mmpS5 778824 p.Ile28Val missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.33
Rv1258c 1406138 c.1203C>A synonymous_variant 0.12
Rv1258c 1406259 p.Pro361Leu missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102417 p.Ala209Val missense_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168712 p.Ala634Val missense_variant 0.11
PPE35 2169157 p.Thr486Ala missense_variant 0.2
PPE35 2169890 c.723C>T synonymous_variant 0.17
PPE35 2169893 c.720C>A synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.21
PPE35 2169910 p.Asn235Tyr missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518066 c.-49A>G upstream_gene_variant 0.25
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474836 p.Glu277Gly missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840232 p.Arg397Cys missense_variant 0.12
alr 3840445 p.Leu326Met missense_variant 0.15
alr 3840571 p.Val284Met missense_variant 0.13
clpC1 4038162 p.Arg848Leu missense_variant 0.25
embC 4240312 c.450G>A synonymous_variant 0.14
embC 4240956 p.Pro365Leu missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245664 p.Gly811Asp missense_variant 0.12
embB 4249323 p.Ala937Glu missense_variant 0.18
embB 4249339 c.2826T>C synonymous_variant 0.11
embB 4249369 c.2856T>C synonymous_variant 0.12
embB 4249376 c.2863C>T synonymous_variant 0.12
embB 4249381 c.2868A>G synonymous_variant 0.12
embB 4249396 c.2883C>T synonymous_variant 0.15
embB 4249405 c.2892C>G synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.8
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408193 p.Ile4Val missense_variant 0.15