TB-Profiler result

Run: ERR4796743
Summary

Run ID: ERR4796743

Sample name:

Date: 20-10-2023 01:53:52

Number of reads: 6431818

Percentage reads mapped: 99.58

Strain: lineage2.2.1;lineage1.2.2.2

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 (0.76)
Isoniazid R katG p.Ser315Thr (0.70)
Ethambutol R embA c.-12C>T (0.74), embB p.Gly406Ser (0.70)
Pyrazinamide R pncA c.-11A>G (0.80)
Streptomycin R rpsL p.Lys43Arg (0.84)
Fluoroquinolones R gyrA p.Ala90Val (0.72)
Moxifloxacin R gyrA p.Ala90Val (0.72)
Ofloxacin R gyrA p.Ala90Val (0.72)
Levofloxacin R gyrA p.Ala90Val (0.72)
Ciprofloxacin R gyrA p.Ala90Val (0.72)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.1390_1391dupGA (0.81), ethA c.1390_1391dupGA (0.81)
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 0.78
lineage1 Indo-Oceanic EAI RD239 0.26
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.8
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.21
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.74
lineage1.2.2.2 Indo-Oceanic NA RD239 0.24
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 0.72 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.76 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.84 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.7 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.8 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 0.74 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.7 ethambutol
ethA 4326082 c.1390_1391dupGA frameshift_variant 0.81 ethionamide, ethionamide
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 0.24
gyrB 6112 p.Met291Ile missense_variant 0.28
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.31
gyrA 9143 c.1842T>C synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.7
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.76
mshA 576108 p.Ala254Gly missense_variant 0.26
ccsA 620625 p.Ile245Met missense_variant 0.78
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.3
rpoC 763886 c.517C>A synonymous_variant 0.31
rpoC 764666 p.Gly433Ser missense_variant 0.78
rpoC 767011 c.3642G>C synonymous_variant 0.26
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.81
mmpL5 777598 c.883C>A synonymous_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 0.84
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.7
embR 1417019 p.Cys110Tyr missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474687 n.1030C>T non_coding_transcript_exon_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 0.76
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.12
Rv1979c 2221725 c.1440T>G synonymous_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.18
eis 2714152 p.Val394Ala missense_variant 0.24
ahpC 2726051 c.-142G>A upstream_gene_variant 0.25
Rv2752c 3064889 p.Lys435Glu missense_variant 0.2
thyA 3074422 p.Pro17Leu missense_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 0.99
Rv3083 3448714 p.Asp71His missense_variant 0.19
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.19
fprA 3475159 p.Asn385Asp missense_variant 0.24
Rv3236c 3612813 p.Thr102Ala missense_variant 0.75
clpC1 4040517 p.Val63Ala missense_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 0.28
embC 4241022 p.Ala387Val missense_variant 0.77
embC 4241042 p.Asn394Asp missense_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.68
embA 4245969 p.Pro913Ser missense_variant 0.21
embB 4247646 p.Glu378Ala missense_variant 0.37
aftB 4267647 p.Asp397Gly missense_variant 0.72
ubiA 4269387 p.Glu149Asp missense_variant 0.24
aftB 4269606 c.-770T>C upstream_gene_variant 0.18
ethA 4326439 p.Asn345Lys missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.23
whiB6 4338635 c.-114A>C upstream_gene_variant 0.26
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.83
gid 4407873 c.330G>T synonymous_variant 0.2
gid 4407927 p.Glu92Asp missense_variant 0.74