TB-Profiler result

Run: ERR4799887
Summary

Run ID: ERR4799887

Sample name:

Date: 01-04-2023 09:26:50

Number of reads: 2855264

Percentage reads mapped: 99.58

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 0.97
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Asn missense_variant 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.95 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.91 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.91 streptomycin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.88 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289228 p.Ile5Ser missense_variant 0.95 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.94 kanamycin
thyA 3074408 p.Thr22Ala missense_variant 0.94 para-aminosalicylic_acid
alr 3840393 p.Met343Thr missense_variant 0.37 cycloserine
embA 4243217 c.-16C>T upstream_gene_variant 0.95 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 491290 p.Val170Met missense_variant 0.95
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.98
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.93
mmpS5 779615 c.-710C>G upstream_gene_variant 0.95
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
rrs 1472310 n.465T>C non_coding_transcript_exon_variant 0.15
rrs 1472527 n.682G>T non_coding_transcript_exon_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.97
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065711 p.Gly161Ser missense_variant 0.13
thyX 3067949 c.-4C>T upstream_gene_variant 0.95
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086944 p.Gly42Asp missense_variant 0.16
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4241022 p.Ala387Val missense_variant 0.91
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247847 p.Gln445Arg missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327283 p.Phe64Ser missense_variant 0.95
whiB6 4338292 p.Ala77Val missense_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.93
gid 4407927 p.Glu92Asp missense_variant 0.97