TB-Profiler result

Run: SRR14782568

Summary

Run ID: SRR14782568

Sample name:

Date: 03-04-2023 11:30:51

Number of reads: 3945186

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.98 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.97 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 0.98 para-aminosalicylic_acid
thyA 3073808 p.Arg222Gly missense_variant 0.98 para-aminosalicylic_acid
alr 3840393 p.Met343Thr missense_variant 1.0 cycloserine
embB 4247429 p.Met306Val missense_variant 0.99 ethambutol
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 0.99
mshA 576113 p.Arg256Gly missense_variant 0.24
mshA 576613 c.1266A>C synonymous_variant 0.34
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764337 p.Glu323Gly missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766779 p.Glu1137Gly missense_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 0.99
mmpS5 779615 c.-710C>G upstream_gene_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476091 n.2434T>C non_coding_transcript_exon_variant 0.99
fabG1 1673553 p.Asp38Glu missense_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 0.99
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 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288797 c.436_444dupGCGGTACGC conservative_inframe_insertion 0.95
kasA 2519071 p.Asp319Glu missense_variant 0.18
pepQ 2860159 p.Ala87Gly missense_variant 0.21
Rv2752c 3064823 p.Val457Leu missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087818 p.Cys333Trp missense_variant 0.12
fbiD 3339734 p.Ala206Gly missense_variant 0.42
fbiD 3339746 p.Ala210Gly missense_variant 0.3
fbiD 3339751 p.Ala212Pro missense_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.22
whiB7 3568431 c.249C>G synonymous_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99
fbiB 3641810 c.276G>C synonymous_variant 1.0
rpoA 3878590 c.-83G>C upstream_gene_variant 0.17
rpoA 3878597 c.-90G>C upstream_gene_variant 0.5
rpoA 3878640 c.-133G>C upstream_gene_variant 0.14
rpoA 3878641 c.-134C>G upstream_gene_variant 0.67
embC 4240409 p.Pro183Ala missense_variant 0.38
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.35
embB 4246529 p.Ser6Arg missense_variant 0.25
embB 4247020 c.507C>G synonymous_variant 0.29
embB 4248328 c.1815G>C synonymous_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 0.98
ubiA 4269391 p.Val148Ala missense_variant 0.99
ethA 4326339 p.Asn379Asp missense_variant 0.99
whiB6 4338200 p.Asp108His missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407927 p.Glu92Asp missense_variant 1.0