TB-Profiler result

Run: ERR4800622
Summary

Run ID: ERR4800622

Sample name:

Date: 01-04-2023 09:57:18

Number of reads: 3787033

Percentage reads mapped: 99.53

Strain: lineage3;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
lineage3 East-African-Indian CAS RD750 0.2
lineage2 East-Asian Beijing RD105 0.82
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.77
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.81
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 7572 p.Ser91Pro missense_variant 0.79 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asn missense_variant 0.11 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.88 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.86 streptomycin
katG 2155168 p.Ser315Asn missense_variant 0.99 isoniazid
pncA 2288830 p.Cys138Arg missense_variant 0.84 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.81 ethambutol
ethA 4327304 p.Ser57Tyr missense_variant 0.84 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 0.99
gyrA 8056 p.Arg252Leu missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.77
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.77
mshA 576108 p.Ala254Gly missense_variant 0.16
mshA 576482 p.Val379Leu missense_variant 0.16
ccsA 620625 p.Ile245Met missense_variant 0.83
rpoB 759746 c.-61C>T upstream_gene_variant 0.25
rpoC 762434 c.-936T>G upstream_gene_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764533 c.1164C>A synonymous_variant 0.84
rpoC 764840 p.Ile491Val missense_variant 0.77
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.84
mmpS5 779615 c.-710C>G upstream_gene_variant 0.79
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.78
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.76
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156389 c.-279dupT upstream_gene_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.15
pncA 2289365 c.-125delC upstream_gene_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 0.25
ribD 2987203 p.Arg122Lys missense_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.86
Rv3236c 3613307 c.-191G>T upstream_gene_variant 0.14
rpoA 3878637 c.-130G>C upstream_gene_variant 0.26
embC 4241022 p.Ala387Val missense_variant 0.86
embC 4242075 p.Arg738Gln missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.79
embB 4246584 p.Arg24Pro missense_variant 0.3
embB 4248324 p.Ala604Gly missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 0.8
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.83
gid 4407927 p.Glu92Asp missense_variant 0.82