TB-Profiler result

Run: ERR10762311
Summary

Run ID: ERR10762311

Sample name:

Date: 31-03-2023 11:03:04

Number of reads: 4350077

Percentage reads mapped: 99.5

Strain: lineage4.2.1;lineage2.2.1

Drug-resistance: Pre-XDR-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 0.37
lineage4 Euro-American LAM;T;S;X;H None 0.65
lineage4.2 Euro-American H;T;LAM None 0.66
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.38
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.33
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.64
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 7582 p.Asp94Ala missense_variant 0.55 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.32 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.67 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.66 isoniazid, ethionamide
tlyA 1918415 p.Ser159* stop_gained 0.67 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289218 p.Asp8Glu missense_variant 0.39 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.62 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.64 kanamycin
ald 3087252 c.436_437dupGC frameshift_variant 0.55 cycloserine
embA 4243217 c.-16C>T upstream_gene_variant 0.39 ethambutol
embB 4247399 p.Asn296His missense_variant 0.39 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.62 ethambutol
ethA 4327363 c.110delA frameshift_variant 0.31 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.65
fgd1 491742 c.960T>C synonymous_variant 0.37
mshA 575907 p.Ala187Val missense_variant 0.32
mshA 576108 p.Ala254Gly missense_variant 0.25
ccsA 619969 p.Val27Ile missense_variant 0.78
ccsA 620625 p.Ile245Met missense_variant 0.3
rpoB 762391 p.Leu862Arg missense_variant 0.66
rpoC 763031 c.-339T>C upstream_gene_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.31
mmpL5 776182 p.Asp767Asn missense_variant 0.36
mmpS5 779615 c.-710C>G upstream_gene_variant 0.32
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.37
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.16
rpsA 1833813 p.Leu91Arg missense_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.35
PPE35 2167926 p.Leu896Ser missense_variant 0.41
PPE35 2169879 p.Phe245Cys missense_variant 0.62
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
pepQ 2860159 p.Ala87Gly missense_variant 0.18
ald 3086731 c.-89A>G upstream_gene_variant 0.4
ald 3086742 c.-78A>C upstream_gene_variant 0.6
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.5
Rv3083 3448859 c.359dupG frameshift_variant 0.42
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.34
rpoA 3878416 p.Gly31Ala missense_variant 0.34
rpoA 3878637 c.-130G>C upstream_gene_variant 0.22
rpoA 3878641 c.-134C>G upstream_gene_variant 0.66
embC 4240409 p.Pro183Ala missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.33
embA 4243460 c.228C>T synonymous_variant 0.36
embB 4246584 p.Arg24Pro missense_variant 0.29
embB 4248324 p.Ala604Gly missense_variant 0.2
embB 4249594 c.3081G>A synonymous_variant 0.7
aftB 4267647 p.Asp397Gly missense_variant 0.26
ethA 4326632 p.His281Pro missense_variant 0.69
ethA 4328376 c.-903G>C upstream_gene_variant 0.65
whiB6 4338371 p.Thr51Pro missense_variant 0.33
whiB6 4338594 c.-73T>A upstream_gene_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.36
gid 4407927 p.Glu92Asp missense_variant 0.34