TB-Profiler result

Run: ERR5866149
Summary

Run ID: ERR5866149

Sample name:

Date: 02-04-2023 00:32:01

Number of reads: 1337734

Percentage reads mapped: 99.37

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 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
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 781822 p.Lys88Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155795 p.Ala106Val missense_variant 0.13 isoniazid
pncA 2289030 p.His71Arg missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247513 p.Tyr334His missense_variant 1.0 ethambutol
thyA 3072600 c.-4122_*1079del transcript_ablation 1.0 para-aminosalicylic_acid
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 575185 c.-163C>T upstream_gene_variant 0.2
mshA 575312 c.-36G>A upstream_gene_variant 0.15
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576782 c.1439_1440delCG frameshift_variant 0.1
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761817 c.2011C>A synonymous_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833568 c.27G>T synonymous_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917979 p.Arg14Gly missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156570 c.-459C>T upstream_gene_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168797 p.Thr606Ala missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289355 c.-116_-115delGG upstream_gene_variant 0.17
eis 2714918 p.Glu139* stop_gained 0.12
thyX 3067949 c.-4C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087532 p.Ala238Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474414 c.408A>G synonymous_variant 0.11
fprA 3475008 c.1002C>T synonymous_variant 0.18
fprA 3475016 p.Gln337Arg missense_variant 0.17
Rv3236c 3612229 c.888C>T synonymous_variant 0.92
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613032 p.Ala29Thr missense_variant 0.2
Rv3236c 3613222 c.-106T>C upstream_gene_variant 0.13
fbiB 3641898 p.Pro122Thr missense_variant 0.1
fbiB 3642141 p.Asp203Asn missense_variant 0.12
fbiB 3642701 c.1167C>T synonymous_variant 0.12
clpC1 4038955 p.Glu584* stop_gained 0.18
embC 4240723 c.865delG frameshift_variant 0.14
embA 4242532 c.-701A>G upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243862 c.630C>A synonymous_variant 0.1
embA 4244166 p.Ala312Thr missense_variant 0.18
embA 4245942 p.Arg904Ser missense_variant 0.17
embB 4246803 c.292delG frameshift_variant 0.17
embB 4249744 p.Gln1077His missense_variant 0.67
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268538 p.Leu100Pro missense_variant 0.15
ubiA 4269754 p.Val27Glu missense_variant 0.18
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
gid 4408382 c.-180A>T upstream_gene_variant 0.13