TB-Profiler result

Run: ERR10869423
Summary

Run ID: ERR10869423

Sample name:

Date: 31-03-2023 11:21:23

Number of reads: 3616404

Percentage reads mapped: 99.65

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 0.99
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 0.51 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.48 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.42 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.55 rifampicin
rpoC 766022 p.Ile885Val missense_variant 0.12 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.46 streptomycin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.52 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 0.53 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289067 p.Ser59Pro missense_variant 0.45 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.57 kanamycin, amikacin
eis 2715369 c.-37G>T upstream_gene_variant 0.43 kanamycin
folC 2747141 p.Glu153Gly missense_variant 0.54 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.59 ethambutol
ethA 4326183 c.1290delC frameshift_variant 0.44 ethionamide, ethionamide
ethA 4326705 c.768delG frameshift_variant 0.61 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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765036 p.Arg556Leu missense_variant 0.49
rpoC 766645 p.Glu1092Asp missense_variant 0.65
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 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.14
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
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 2169016 p.Thr533Ala missense_variant 0.46
PPE35 2170035 p.Val193Ala missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.48
PPE35 2170053 p.Thr187Ser missense_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715330 c.3G>A synonymous_variant 0.57
folC 2746747 c.852G>C synonymous_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878567 c.-60C>G upstream_gene_variant 0.35
rpoA 3878599 c.-92C>G upstream_gene_variant 0.17
rpoA 3878639 c.-132C>G upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.28
embB 4246548 p.Pro12Gln missense_variant 0.32
embB 4246555 c.42G>C synonymous_variant 0.3
embB 4246556 p.Ala15Pro missense_variant 0.3
embB 4246563 p.Leu17Trp missense_variant 0.3
embB 4246567 c.54G>T synonymous_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 0.99
whiB6 4338563 c.-42G>T upstream_gene_variant 0.61
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