TB-Profiler result

Run: SRR23310936
Summary

Run ID: SRR23310936

Sample name:

Date: 14-03-2023 03:45:05

Number of reads: 3598648

Percentage reads mapped: 99.59

Strain: lineage2.2

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
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
gyrB 6737 p.Thr500Pro missense_variant 0.11 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 0.14 rifampicin
rpoB 761110 p.Asp435Gly missense_variant 0.11 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.91 rifampicin
rpoB 762089 p.Glu761Asp missense_variant 0.91 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.11 streptomycin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.99 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.11 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2289100 p.Lys48Glu missense_variant 0.91 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
embB 4247553 p.Ser347Ile missense_variant 0.13 ethambutol
embB 4247574 p.Asp354Ala missense_variant 0.88 ethambutol
ethA 4327480 c.-7T>C upstream_gene_variant 0.9 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 7581 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.21
fgd1 491742 c.960T>C synonymous_variant 0.98
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576613 c.1266A>C synonymous_variant 0.18
mshA 576616 c.1269G>C synonymous_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 0.99
mmpL5 777883 p.Gly200Arg missense_variant 0.17
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.19
rpsA 1834177 c.636A>C synonymous_variant 0.97
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087818 p.Cys333Trp missense_variant 0.12
fbiD 3339734 p.Ala206Gly missense_variant 0.69
fbiD 3339751 p.Ala212Pro missense_variant 0.14
fprA 3473996 c.-10_-9insA upstream_gene_variant 0.99
whiB7 3568428 c.252A>G synonymous_variant 0.26
Rv3236c 3612701 p.Asp139Gly missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878597 c.-90G>C upstream_gene_variant 0.42
rpoA 3878641 c.-134C>G upstream_gene_variant 0.71
embC 4240409 p.Pro183Ala missense_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 0.89
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.22
embB 4246584 p.Arg24Pro missense_variant 0.13
embB 4248328 c.1815G>C synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338563 c.-42G>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407927 p.Glu92Asp missense_variant 0.98