TB-Profiler result

Run: ERR019556

Summary

Run ID: ERR019556

Sample name:

Date: 18-08-2022 11:49:55

Number of reads: 1498656

Percentage reads mapped: 98.24

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 0.99
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 0.6 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.33 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.92 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
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 0.91
mshA 575907 p.Ala187Val missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765462 p.Asn698Ser missense_variant 0.17
rpoC 766645 p.Glu1092Asp missense_variant 0.92
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474928 n.1271C>A non_coding_transcript_exon_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 0.91
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
embC 4239842 c.-21C>A upstream_gene_variant 0.18
ethA 4327247 p.Ala76Asp missense_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0