TB-Profiler result

Run: ERR8665555
Summary

Run ID: ERR8665555

Sample name:

Date: 02-04-2023 07:31:46

Number of reads: 831105

Percentage reads mapped: 99.55

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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289040 p.Trp68Gly missense_variant 1.0 pyrazinamide
folC 2747471 p.Ile43Ser missense_variant 1.0 para-aminosalicylic_acid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326087 c.1386delA 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 1.0
gyrA 9642 p.Gly781Cys missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 0.93
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576456 p.Val370Glu missense_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764283 p.Ser305* stop_gained 0.2
rpoC 765704 p.Lys779Glu missense_variant 0.12
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
rplC 801211 p.Gln135Lys missense_variant 0.19
fbiC 1303526 p.Ser199Trp missense_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834495 p.Glu318Asp missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.95
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986917 p.Glu27* stop_gained 0.18
Rv2752c 3064808 p.Leu462Met missense_variant 0.13
Rv2752c 3065910 c.282C>A synonymous_variant 0.19
Rv2752c 3066304 c.-113C>A upstream_gene_variant 0.18
thyX 3067710 p.Ser79Leu missense_variant 0.18
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568795 c.-116A>G upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641504 p.Arg321Leu missense_variant 0.13
fbiB 3641537 c.3G>T start_lost 0.23
fbiB 3641695 p.Ser54Tyr missense_variant 0.17
fbiB 3641745 p.Asp71Asn missense_variant 0.17
ddn 3986675 c.-169G>T upstream_gene_variant 0.17
clpC1 4040179 p.Arg176Ser missense_variant 0.2
embC 4242074 c.2212C>A synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242663 p.Ser934Tyr missense_variant 0.22
embC 4242812 p.Asp984Tyr missense_variant 0.23
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244571 p.Arg447Trp missense_variant 0.2
embA 4244814 p.Leu528Met missense_variant 0.14
embA 4246297 p.Gln1022Arg missense_variant 0.1
embB 4247325 p.Ala271Glu missense_variant 0.13
ubiA 4269239 p.Ala199Thr missense_variant 0.13
ethA 4328019 c.-546G>T upstream_gene_variant 0.14
whiB6 4338371 p.Thr51Pro missense_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