TB-Profiler result

Run: SRR23862005
Summary

Run ID: SRR23862005

Sample name:

Date: 12-04-2023 14:25:25

Number of reads: 2888770

Percentage reads mapped: 99.55

Strain: lineage4.2.1;lineage2.2.1

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (0.73)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.72)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.29
lineage4.2 Euro-American H;T;LAM None 0.74
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.26
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.2
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.75
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
rpsL 781687 p.Lys43Arg missense_variant 0.72 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.73 isoniazid
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 0.34
mshA 575907 p.Ala187Val missense_variant 0.21
mshA 576108 p.Ala254Gly missense_variant 0.17
mshA 576453 p.Val369Gly missense_variant 0.21
ccsA 620625 p.Ile245Met missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 0.24
rpoC 766645 p.Glu1092Asp missense_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.33
mmpL5 776182 p.Asp767Asn missense_variant 0.3
mmpL5 777883 p.Gly200Arg missense_variant 0.19
mmpS5 779615 c.-710C>G upstream_gene_variant 0.27
rpsL 781395 c.-165T>C upstream_gene_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 0.24
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.27
PPE35 2167926 p.Leu896Ser missense_variant 0.18
PPE35 2169879 p.Phe245Cys missense_variant 0.71
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519006 p.Ala298Ser missense_variant 0.24
kasA 2519071 p.Asp319Glu missense_variant 0.17
pepQ 2860159 p.Ala87Gly missense_variant 0.21
ald 3086742 c.-78A>C upstream_gene_variant 0.76
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.8
Rv3083 3448456 c.-48G>A upstream_gene_variant 0.77
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.3
whiB7 3568431 c.249C>G synonymous_variant 0.38
Rv3236c 3612813 p.Thr102Ala missense_variant 0.33
rpoA 3878590 c.-83G>C upstream_gene_variant 0.29
rpoA 3878641 c.-134C>G upstream_gene_variant 0.67
clpC1 4038932 c.1773G>A synonymous_variant 0.82
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.29
embB 4246527 p.Ala5Gly missense_variant 0.2
embB 4246584 p.Arg24Pro missense_variant 0.29
embB 4249594 c.3081G>A synonymous_variant 0.75
aftB 4267647 p.Asp397Gly missense_variant 0.24
ethA 4328376 c.-903G>C upstream_gene_variant 0.77
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.27
gid 4407927 p.Glu92Asp missense_variant 0.33