TB-Profiler result

Run: ERR4797047
Summary

Run ID: ERR4797047

Sample name:

Date: 01-04-2023 07:19:22

Number of reads: 3820925

Percentage reads mapped: 99.67

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 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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289031 p.His71Tyr missense_variant 1.0 pyrazinamide
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326231 c.1242delT frameshift_variant 1.0 ethionamide, 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576113 p.Arg256Gly missense_variant 0.44
ccsA 619725 c.-166C>G upstream_gene_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762285 p.Arg827Cys missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
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
Rv1258c 1407489 c.-149G>A upstream_gene_variant 0.13
embR 1416878 c.469delC frameshift_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471793 n.-53G>T upstream_gene_variant 0.33
rrs 1471805 n.-41C>A upstream_gene_variant 0.75
rrl 1474574 n.917A>T non_coding_transcript_exon_variant 0.33
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.22
fabG1 1673553 p.Asp38Glu missense_variant 0.3
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102817 p.Leu76Val missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168693 p.Asn640Lys missense_variant 0.15
PPE35 2170390 p.Trp75Gly missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.23
eis 2714846 p.Val163Ile missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.2
Rv2752c 3065090 c.1101delA frameshift_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>A synonymous_variant 0.11
fbiD 3339734 p.Ala206Gly missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474213 p.Lys69Asn missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4040240 c.465C>A synonymous_variant 0.5
clpC1 4040295 p.Gln137Pro missense_variant 0.25
embC 4242131 p.Val757Leu missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245835 p.Leu868Arg missense_variant 0.22
embA 4246143 p.Ile971Phe missense_variant 0.25
embB 4247100 p.Ala196Val missense_variant 0.12
embB 4247424 p.Leu304Pro missense_variant 0.15
embB 4247880 p.Val456Ala missense_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 0.98
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267902 p.Val312Gly missense_variant 0.43
aftB 4267930 p.Arg303Gly missense_variant 0.12
aftB 4268619 p.Val73Gly missense_variant 0.31
ethA 4326271 c.1203T>C synonymous_variant 0.1
whiB6 4338323 c.198dupC frameshift_variant 1.0
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