TB-Profiler result

Run: SRR1049047
Summary

Run ID: SRR1049047

Sample name:

Date: 02-04-2023 17:53:00

Number of reads: 2683963

Percentage reads mapped: 99.36

Strain: lineage2.2.2

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
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
pncA 2289100 p.Lys48Glu missense_variant 0.98 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
ahpC 2726139 c.-54C>T upstream_gene_variant 1.0 isoniazid
folC 2747454 p.Arg49Trp missense_variant 1.0 para-aminosalicylic_acid
embB 4248003 p.Gln497Pro missense_variant 1.0 ethambutol
ethA 4327317 c.156_157insT frameshift_variant 1.0 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 7584 p.Ser95Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575531 p.Thr62Phe missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778743 p.Val55Met missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781406 c.-154_-153insC upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833909 p.Asp123Ala missense_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834482 p.Glu314Gly missense_variant 1.0
tlyA 1917959 p.Val7Gly missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102140 c.903C>T synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155969 p.Leu48Arg missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222395 p.Pro257Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3074122 p.Asp117Gly missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640372 c.-171A>G upstream_gene_variant 0.99
alr 3840952 p.Lys157Glu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly 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
Rv3236c 3611303 c.-2954_*655del transcript_ablation 1.0