TB-Profiler result

Run: ERR4799753
Summary

Run ID: ERR4799753

Sample name:

Date: 01-04-2023 09:20:54

Number of reads: 3880321

Percentage reads mapped: 99.57

Strain: lineage2.2.1.1

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 0.89
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.9
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.9
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.9
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 0.83 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 0.84 rifampicin
rpoB 761110 p.Asp435Gly missense_variant 0.8 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.89 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.89 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 0.93 para-aminosalicylic_acid
embA 4243221 c.-12C>T upstream_gene_variant 0.87 ethambutol
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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.93
ccsA 620625 p.Ile245Met missense_variant 0.88
rpoB 759746 c.-61C>T upstream_gene_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 0.88
mmpS5 779615 c.-710C>G upstream_gene_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
Rv1258c 1406760 c.580_581insC frameshift_variant 0.91
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.96
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 0.95
Rv2752c 3066303 c.-112C>T upstream_gene_variant 0.15
thyA 3074177 p.Arg99* stop_gained 0.9
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
Rv3236c 3612813 p.Thr102Ala missense_variant 0.85
embC 4242075 p.Arg738Gln missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.88
embB 4247880 p.Val456Ala missense_variant 0.9
embB 4248115 c.1602C>T synonymous_variant 0.92
aftB 4267647 p.Asp397Gly missense_variant 0.84
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.95