TB-Profiler result

Run: ERR221569
Summary

Run ID: ERR221569

Sample name:

Date: 20-10-2023 23:02:36

Number of reads: 2942872

Percentage reads mapped: 94.57

Strain: lineage1.2.2.1

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
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 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.1 Indo-Oceanic NA RD239 1.0
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
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 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8489 c.1188A>G synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491060 p.Met93Thr missense_variant 0.97
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620659 p.Arg257Cys missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
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
rplC 800899 p.Ala31Thr missense_variant 0.98
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 1.0
rrs 1472555 n.710C>T non_coding_transcript_exon_variant 0.59
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.4
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.47
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.49
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.47
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.54
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.55
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.45
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.23
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.23
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.23
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.23
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.24
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.23
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.23
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.24
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.23
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.24
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.25
rrs 1473201 n.1356_1357delACinsT non_coding_transcript_exon_variant 0.2
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.19
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.34
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.39
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.43
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.43
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.51
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.44
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.41
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.34
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.26
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.27
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.21
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.18
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.25
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.27
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.31
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.38
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.52
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.52
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.51
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.54
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.49
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.5
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.35
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.28
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
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.98
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246870 c.357C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethR 4327450 c.-99G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0