TB-Profiler result

Run: ERR4797284
Summary

Run ID: ERR4797284

Sample name:

Date: 20-10-2023 02:16:52

Number of reads: 4232004

Percentage reads mapped: 99.5

Strain: lineage2.2.1;lineage1.1.2

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
Rifampicin R rpoB p.Ser450Leu (0.13)
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.14)
Fluoroquinolones R gyrA p.Ala90Val (0.15)
Moxifloxacin R gyrA p.Ala90Val (0.15)
Ofloxacin R gyrA p.Ala90Val (0.15)
Levofloxacin R gyrA p.Ala90Val (0.15)
Ciprofloxacin R gyrA p.Ala90Val (0.15)
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 0.11
lineage1 Indo-Oceanic EAI RD239 0.9
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.88
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.08
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.89
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.08
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 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.13 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.14 streptomycin
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 0.87
gyrB 6124 c.885C>T synonymous_variant 0.86
gyrA 7153 c.-149G>C upstream_gene_variant 0.89
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.89
gyrA 9143 c.1842T>C synonymous_variant 0.85
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.14
ccsA 620553 c.663T>C synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.87
rpoC 763886 c.517C>A synonymous_variant 0.87
rpoC 764817 p.Val483Ala missense_variant 0.19
rpoC 765171 p.Pro601Leu missense_variant 0.87
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779323 p.Ala112Ser missense_variant 0.83
mmpR5 779414 p.Leu142Arg missense_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406503 p.Val280Leu missense_variant 0.93
embR 1417019 p.Cys110Tyr missense_variant 0.88
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475300 n.1643G>T non_coding_transcript_exon_variant 0.86
rpsA 1834177 c.636A>C synonymous_variant 0.19
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 2167983 p.Gly877Asp missense_variant 0.87
PPE35 2169813 c.794_799dupACAACT conservative_inframe_insertion 0.83
Rv1979c 2222308 p.Asp286Gly missense_variant 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.89
ahpC 2726051 c.-142G>A upstream_gene_variant 0.88
Rv2752c 3064632 c.1560C>T synonymous_variant 0.89
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087824 c.1005G>A synonymous_variant 0.92
Rv3083 3448714 p.Asp71His missense_variant 0.94
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.9
fprA 3475159 p.Asn385Asp missense_variant 0.87
whiB7 3568795 c.-116A>G upstream_gene_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 0.96
embC 4240671 p.Thr270Ile missense_variant 0.87
embC 4241042 p.Asn394Asp missense_variant 0.86
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.9
embA 4245385 p.Thr718Ile missense_variant 0.92
embA 4245969 p.Pro913Ser missense_variant 0.92
embB 4247646 p.Glu378Ala missense_variant 0.87
embB 4249757 p.Thr1082Ala missense_variant 0.16
aftB 4267647 p.Asp397Gly missense_variant 0.1
ubiA 4269387 p.Glu149Asp missense_variant 0.93
aftB 4269606 c.-770T>C upstream_gene_variant 0.88
whiB6 4338224 c.297delC frameshift_variant 0.87
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.9
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.87
gid 4407927 p.Glu92Asp missense_variant 0.14