TB-Profiler result

Run: SRR18714922
Summary

Run ID: SRR18714922

Sample name:

Date: 03-04-2023 20:10:50

Number of reads: 4205975

Percentage reads mapped: 99.52

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.Asp94Ala missense_variant 0.85 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764822 p.Asp485Asn missense_variant 0.12 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
katG 2155109 p.Ile335Val missense_variant 0.19 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288703 p.Val180Gly missense_variant 0.18 pyrazinamide
pncA 2288841 p.Ala134Val missense_variant 0.8 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.86 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.2 ethambutol
ethA 4326435 p.Gln347* stop_gained 0.87 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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.83
mshA 576108 p.Ala254Gly missense_variant 0.41
mshA 576456 p.Val370Gly missense_variant 0.26
ccsA 620625 p.Ile245Met missense_variant 0.9
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 0.81
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.84
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302917 c.-14_-13insA upstream_gene_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
fabG1 1673553 p.Asp38Glu missense_variant 0.26
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834776 p.Ala412Val missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.22
thyX 3067936 p.Thr4Pro missense_variant 0.12
thyX 3067963 c.-19_-18insAC upstream_gene_variant 0.54
thyX 3067969 c.-24G>T upstream_gene_variant 0.58
thyX 3067970 c.-25T>C upstream_gene_variant 0.66
thyA 3074393 c.73_78delGGAACC conservative_inframe_deletion 0.82
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.69
fbiD 3339746 p.Ala210Gly missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640879 c.-656C>T upstream_gene_variant 0.2
rpoA 3877960 p.Val183Ala missense_variant 0.81
rpoA 3878597 c.-90G>C upstream_gene_variant 0.33
rpoA 3878641 c.-134C>G upstream_gene_variant 0.36
embC 4240409 p.Pro183Ala missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243598 c.366G>A synonymous_variant 0.18
embB 4246527 p.Ala5Gly missense_variant 0.34
embB 4246584 p.Arg24Pro missense_variant 0.26
embB 4247872 c.1359C>T synonymous_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326474 p.Pro334Ala missense_variant 0.15
whiB6 4338286 p.Val79Ala missense_variant 0.84
whiB6 4338326 p.Ala66Thr missense_variant 0.21
whiB6 4338563 c.-42G>T upstream_gene_variant 0.83
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