TB-Profiler result

Run: ERR2515255
Summary

Run ID: ERR2515255

Sample name:

Date: 31-03-2023 20:50:15

Number of reads: 701224

Percentage reads mapped: 99.68

Strain: lineage4.1.2;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 0.86
lineage4 Euro-American LAM;T;S;X;H None 0.17
lineage4.1 Euro-American T;X;H None 0.05
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.86
lineage4.1.2 Euro-American T;H None 0.1
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.87
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 0.19 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 0.2 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.15 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.2 isoniazid
pncA 2289031 p.His71Tyr missense_variant 0.14 pyrazinamide
embA 4243217 c.-16C>G upstream_gene_variant 0.13 ethambutol
gid 4407802 p.Ala134Glu missense_variant 0.2 streptomycin
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 491591 p.Lys270Met missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 0.77
mshA 575907 p.Ala187Val missense_variant 0.78
ccsA 620625 p.Ile245Met missense_variant 0.77
rpoB 760115 c.309C>T synonymous_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 0.85
mmpL5 775639 p.Ile948Val missense_variant 0.97
mmpL5 776100 p.Thr794Ile missense_variant 0.94
mmpL5 776182 p.Asp767Asn missense_variant 0.96
mmpS5 779615 c.-710C>G upstream_gene_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302976 p.Val16Ile missense_variant 0.85
fbiC 1304846 p.Ala639Val missense_variant 0.67
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 0.85
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.86
PPE35 2167926 p.Leu896Ser missense_variant 0.81
PPE35 2168607 p.Met669Arg missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290110 c.-869C>T upstream_gene_variant 0.85
kasA 2518076 c.-39C>T upstream_gene_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.86
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.1
embA 4243460 c.228C>T synonymous_variant 0.83
embA 4244184 p.Ser318Arg missense_variant 0.1
embA 4245745 p.Pro838Leu missense_variant 0.73
embB 4246567 c.54G>T synonymous_variant 0.92
embB 4247738 p.Ala409Pro missense_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 0.79
ethA 4326842 p.Tyr211Ser missense_variant 0.19
ethR 4328102 c.555_560delGTCATT disruptive_inframe_deletion 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.86
gid 4407927 p.Glu92Asp missense_variant 0.82