TB-Profiler result

Run: SRR2100207
Summary

Run ID: SRR2100207

Sample name:

Date: 19-10-2023 15:39:18

Number of reads: 5735119

Percentage reads mapped: 99.35

Strain: lineage3;lineage1.2.2.2

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 (0.30)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.27)
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
lineage3 East-African-Indian CAS RD750 0.29
lineage1 Indo-Oceanic EAI RD239 0.72
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.73
lineage1.2.2.2 Indo-Oceanic NA RD239 0.72
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 0.27 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.3 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 5075 c.-165C>T upstream_gene_variant 0.69
gyrB 6112 p.Met291Ile missense_variant 0.8
gyrA 7268 c.-34C>T upstream_gene_variant 0.65
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 8452 p.Ala384Val missense_variant 0.69
gyrA 8668 p.Ala456Val missense_variant 0.65
gyrA 9143 c.1842T>C synonymous_variant 0.69
gyrA 9304 p.Gly668Asp missense_variant 0.99
gyrA 9801 p.Asp834Asn missense_variant 0.72
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.32
rpoC 762434 c.-936T>G upstream_gene_variant 0.3
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.76
rpoC 763886 c.517C>A synonymous_variant 0.76
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.79
rrs 1471659 n.-187C>T upstream_gene_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 2168742 p.Gly624Asp missense_variant 0.72
Rv1979c 2222308 p.Asp286Gly missense_variant 0.68
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.23
pncA 2289348 c.-107T>G upstream_gene_variant 0.29
pncA 2289365 c.-125delC upstream_gene_variant 0.31
kasA 2518132 c.18C>T synonymous_variant 0.78
ahpC 2726051 c.-142G>A upstream_gene_variant 0.72
ahpC 2726105 c.-88G>A upstream_gene_variant 0.3
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339592 p.His159Asn missense_variant 0.8
Rv3083 3448714 p.Asp71His missense_variant 0.68
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.73
fprA 3475159 p.Asn385Asp missense_variant 0.75
alr 3841473 c.-53G>A upstream_gene_variant 0.32
clpC1 4040517 p.Val63Ala missense_variant 0.75
embC 4240671 p.Thr270Ile missense_variant 0.78
embC 4241042 p.Asn394Asp missense_variant 0.76
embC 4242075 p.Arg738Gln missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4245969 p.Pro913Ser missense_variant 0.72
embB 4247646 p.Glu378Ala missense_variant 0.73
ubiA 4269387 p.Glu149Asp missense_variant 0.73
aftB 4269606 c.-770T>C upstream_gene_variant 0.67
ethA 4326148 c.1326G>T synonymous_variant 0.72
ethA 4326439 p.Asn345Lys missense_variant 0.7
ethA 4327672 c.-199G>A upstream_gene_variant 0.25
whiB6 4338203 p.Arg107Cys missense_variant 0.76
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.7
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407742 p.Arg154Pro missense_variant 0.69
gid 4407873 c.330G>T synonymous_variant 0.68