TB-Profiler result

Run: SRR16157105
Summary

Run ID: SRR16157105

Sample name:

Date: 03-04-2023 16:44:24

Number of reads: 838233

Percentage reads mapped: 81.97

Strain: 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 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
gyrA 7581 p.Asp94Asn missense_variant 0.84 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.97 isoniazid, ethionamide
pncA 2288933 p.Tyr103* stop_gained 1.0 pyrazinamide
ethR 4327831 p.Ala95Thr missense_variant 1.0 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 5438 p.Val67Ile missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7919 p.Glu206Asp missense_variant 0.22
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
mshA 576119 p.Ala258Pro missense_variant 0.33
mshA 576436 p.Gln363His missense_variant 0.25
mshA 576453 p.Val369Gly missense_variant 0.5
mshA 576456 p.Val370Gly missense_variant 0.75
mshA 576489 p.Val381Gly missense_variant 0.4
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761482 p.Ala559Gly missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763150 p.Phe1115Cys missense_variant 0.15
rpoC 763555 c.186C>T synonymous_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.13
rpoC 766033 p.Glu888Asp missense_variant 0.14
rpoC 766488 p.Pro1040Leu missense_variant 1.0
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 777883 p.Gly200Arg missense_variant 0.25
mmpS5 778979 c.-74G>T upstream_gene_variant 0.5
mmpL5 779116 c.-636G>A upstream_gene_variant 0.23
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 0.24
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834857 p.Glu439Ala missense_variant 0.24
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 2170037 c.576C>G synonymous_variant 0.5
PPE35 2170390 p.Trp75Gly missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289787 c.-546A>C upstream_gene_variant 0.18
kasA 2519071 p.Asp319Glu missense_variant 0.12
thyX 3067944 p.Val1Gly missense_variant 0.3
thyX 3068026 c.-81G>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339751 p.Ala212Pro missense_variant 0.75
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474075 c.69G>A synonymous_variant 0.22
whiB7 3568833 c.-154C>T upstream_gene_variant 1.0
Rv3236c 3612529 c.588C>T synonymous_variant 0.15
Rv3236c 3612544 c.573T>G synonymous_variant 0.16
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878630 c.-123G>C upstream_gene_variant 0.67
rpoA 3878637 c.-130G>C upstream_gene_variant 0.67
rpoA 3878640 c.-133G>C upstream_gene_variant 0.5
clpC1 4040235 p.Gly157Ala missense_variant 0.16
embC 4240409 p.Pro183Ala missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243682 c.450T>G synonymous_variant 0.25
embA 4244324 c.1092T>G synonymous_variant 0.19
embB 4246527 p.Ala5Gly missense_variant 0.22
embB 4247033 p.Ser174Arg missense_variant 0.4
embB 4248328 c.1815G>C synonymous_variant 0.36
aftB 4267644 p.Asp398Ala missense_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268623 p.Trp72Gly missense_variant 0.15
whiB6 4338200 p.Asp108His missense_variant 0.14
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
gid 4408108 p.Glu32Ala missense_variant 0.17
gid 4408174 p.Ala10Val missense_variant 0.94