TB-Profiler result

Run: SRR26159062
Summary

Run ID: SRR26159062

Sample name:

Date: 16-03-2024 13:37:19

Number of reads: 1030283

Percentage reads mapped: 99.02

Strain:

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (0.37), rpoB p.Ile491Phe (0.48)
Isoniazid R katG p.Ser315Thr (0.58)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.58)
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
lineage1 Indo-Oceanic EAI RD239 0.55
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.48
lineage1.2.2.2 Indo-Oceanic NA RD239 0.51
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.37
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
rpoB 761155 p.Ser450Leu missense_variant 0.37 rifampicin
rpoB 761277 p.Ile491Phe missense_variant 0.48 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.58 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.58 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
gyrB 6112 p.Met291Ile missense_variant 0.6
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.4
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.31
rpoC 763886 c.517C>A synonymous_variant 0.33
rpoC 766809 p.Val1147Ala missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.58
mmpS5 779615 c.-710C>G upstream_gene_variant 0.61
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.52
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103137 c.-95A>G upstream_gene_variant 0.44
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.52
Rv1979c 2222308 p.Asp286Gly missense_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289910 c.-669C>T upstream_gene_variant 0.61
ahpC 2726051 c.-142G>A upstream_gene_variant 0.31
Rv2752c 3064889 p.Lys435Glu missense_variant 0.43
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.7
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.61
fprA 3475159 p.Asn385Asp missense_variant 0.34
Rv3236c 3612813 p.Thr102Ala missense_variant 0.5
fbiA 3641404 p.Trp288Arg missense_variant 0.29
clpC1 4040517 p.Val63Ala missense_variant 0.47
embC 4241042 p.Asn394Asp missense_variant 0.57
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.45
embA 4245969 p.Pro913Ser missense_variant 0.62
embB 4248115 c.1602C>T synonymous_variant 0.35
aftB 4267647 p.Asp397Gly missense_variant 0.82
ubiA 4269387 p.Glu149Asp missense_variant 0.47
aftB 4269606 c.-770T>C upstream_gene_variant 0.62
ethA 4326439 p.Asn345Lys missense_variant 0.27
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.66
whiB6 4338635 c.-114A>C upstream_gene_variant 0.61
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.59
gid 4407898 c.273_305delAGAACCGCTACTGCGCCGCACCGAGTTTCTTCGinsC frameshift_variant&missense_variant 0.57
gid 4407898 p.Glu92Asp missense_variant 0.43