TB-Profiler result

Run: ERR5866150
Summary

Run ID: ERR5866150

Sample name:

Date: 02-04-2023 00:32:11

Number of reads: 1586536

Percentage reads mapped: 99.38

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 0.99
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 2155734 p.Met126Ile missense_variant 0.11 isoniazid
pncA 2289030 p.His71Arg missense_variant 0.98 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 491008 c.231delC frameshift_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575567 p.Gln74Lys missense_variant 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619822 c.-69G>T upstream_gene_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620854 p.Gly322Ser missense_variant 0.13
rpoB 762448 p.Gly881Ala missense_variant 0.22
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
mmpL5 777536 c.945G>C synonymous_variant 0.12
mmpL5 779049 c.-569G>A upstream_gene_variant 0.12
mmpS5 779560 c.-655C>G upstream_gene_variant 0.11
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
inhA 1674200 c.-2A>T upstream_gene_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101816 c.1227C>A synonymous_variant 0.15
ndh 2101931 p.Ala371Val missense_variant 0.11
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
folC 2746370 p.Arg410Gln missense_variant 0.12
ribD 2987337 p.Gly167Ser missense_variant 0.12
ribD 2987510 c.672G>A synonymous_variant 0.2
ribD 2987574 p.Asp246Asn missense_variant 0.1
thyX 3067356 p.Ala197Glu missense_variant 0.11
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
Rv3083 3449083 p.Pro194Thr missense_variant 0.17
fprA 3473981 c.-26G>C upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475065 c.1059C>T synonymous_variant 0.11
whiB7 3568666 p.Thr5Lys missense_variant 0.11
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4039007 c.1698G>A synonymous_variant 0.13
panD 4044265 p.Leu6Pro missense_variant 0.1
embC 4241009 p.Gly383Cys missense_variant 0.12
embC 4242428 p.Ala856Ser missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244185 p.Ser318Ile missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268488 p.Met117Val missense_variant 0.1
ubiA 4269303 c.530delT frameshift_variant 0.12
ethA 4327237 p.Lys79Asn missense_variant 0.1
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