TB-Profiler result

Run: ERR4831634
Summary

Run ID: ERR4831634

Sample name:

Date: 20-10-2023 13:55:14

Number of reads: 1335387

Percentage reads mapped: 99.41

Strain: lineage2.2.1;lineage1.1.1

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.Ile317Val (0.37), katG p.Ser315Asn (0.39)
Ethambutol R embB p.Gly406Ala (0.22)
Pyrazinamide R pncA p.Ile5Ser (0.38)
Streptomycin R rpsL p.Lys43Arg (0.45)
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 0.32
lineage1 Indo-Oceanic EAI RD239 0.72
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.72
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.33
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.27
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.64
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 0.45 streptomycin
katG 2155163 p.Ile317Val missense_variant 0.37 isoniazid
katG 2155168 p.Ser315Asn missense_variant 0.39 isoniazid
pncA 2289228 p.Ile5Ser missense_variant 0.38 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.22 ethambutol
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 5627 p.Ala130Ser missense_variant 0.8
gyrB 6112 p.Met291Ile missense_variant 0.76
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.71
gyrA 9143 c.1842T>C synonymous_variant 0.71
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.26
ccsA 620625 p.Ile245Met missense_variant 0.53
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.71
rpoC 763886 c.517C>A synonymous_variant 0.74
rpoC 765171 p.Pro601Leu missense_variant 0.81
rpoC 766487 p.Pro1040Ala missense_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.3
mmpS5 779615 c.-710C>G upstream_gene_variant 0.36
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781694 c.135G>A synonymous_variant 0.56
Rv1258c 1406760 c.580_581insC frameshift_variant 0.38
embR 1417019 p.Cys110Tyr missense_variant 0.62
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473162 n.1317C>T non_coding_transcript_exon_variant 0.88
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.61
rpsA 1834177 c.636A>C synonymous_variant 0.37
rpsA 1834319 p.Val260Ile missense_variant 0.67
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 0.64
PPE35 2168500 p.Ser705Ala missense_variant 0.66
Rv1979c 2222308 p.Asp286Gly missense_variant 0.73
Rv1979c 2223144 p.Arg7Ser missense_variant 0.82
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.55
ahpC 2726051 c.-142G>A upstream_gene_variant 0.86
ahpC 2726763 p.Leu191Phe missense_variant 0.72
Rv2752c 3064632 c.1560C>T synonymous_variant 0.59
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338931 c.-187C>A upstream_gene_variant 0.21
Rv3083 3448714 p.Asp71His missense_variant 0.74
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.78
fprA 3475159 p.Asn385Asp missense_variant 0.87
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22
alr 3840571 p.Val284Leu missense_variant 0.22
rpoA 3878630 c.-124delC upstream_gene_variant 0.82
clpC1 4038545 c.2160C>T synonymous_variant 0.61
clpC1 4040517 p.Val63Ala missense_variant 0.6
embC 4240671 p.Thr270Ile missense_variant 0.69
embC 4241042 p.Asn394Asp missense_variant 0.76
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.41
embA 4243848 p.Val206Met missense_variant 0.63
embA 4244096 c.864C>T synonymous_variant 0.62
embA 4245969 p.Pro913Ser missense_variant 0.71
embB 4247646 p.Glu378Ala missense_variant 0.71
ubiA 4269387 p.Glu149Asp missense_variant 0.73
aftB 4269606 c.-770T>C upstream_gene_variant 0.73
whiB6 4338242 p.Gln94Glu missense_variant 0.77
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.85
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.66
gid 4407927 p.Glu92Asp missense_variant 0.26