TB-Profiler result

Run: ERR176631

Summary

Run ID: ERR176631

Sample name:

Date: 24-01-2024 12:25:09

Number of reads: 3572273

Percentage reads mapped: 84.63

Strain: lineage4;lineage1.1.2

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
lineage4 Euro-American LAM;T;S;X;H None 0.06
lineage1 Indo-Oceanic EAI RD239 0.94
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.95
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.95
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 6112 p.Met291Ile missense_variant 0.96
gyrB 6124 c.885C>T synonymous_variant 0.96
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.92
gyrA 9143 c.1842T>C synonymous_variant 0.92
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763884 p.Ala172Val missense_variant 0.96
rpoC 763886 c.517C>A synonymous_variant 0.96
rpoC 765171 p.Pro601Leu missense_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.92
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.14
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.14
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.22
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.21
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.25
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.24
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.24
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.24
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.17
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.12
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.16
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.18
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.17
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.16
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.17
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.16
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.16
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.16
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.14
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.15
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.17
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.18
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.19
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.19
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.17
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.2
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.21
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.26
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.27
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.32
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.34
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.34
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.39
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.42
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.24
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.19
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.11
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.11
rrl 1476624 n.2967T>G non_coding_transcript_exon_variant 0.11
fabG1 1673283 c.-157A>C upstream_gene_variant 0.91
tlyA 1917777 c.-163A>G upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918106 p.Thr56Ile missense_variant 0.94
katG 2154724 p.Arg463Leu missense_variant 0.98
katG 2155557 c.555C>T synonymous_variant 0.96
PPE35 2167926 p.Leu896Ser missense_variant 0.92
PPE35 2167983 p.Gly877Asp missense_variant 0.92
PPE35 2170378 p.Ala79Thr missense_variant 0.93
Rv1979c 2221783 p.Ala461Glu missense_variant 0.97
Rv1979c 2222308 p.Asp286Gly missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.9
eis 2714199 p.Lys378Asn missense_variant 0.91
ahpC 2726051 c.-142G>A upstream_gene_variant 0.94
ahpC 2726672 c.480G>A synonymous_variant 0.97
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448442 c.-62A>C upstream_gene_variant 0.95
Rv3083 3448714 p.Asp71His missense_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.92
fprA 3475159 p.Asn385Asp missense_variant 0.99
Rv3236c 3613012 c.105G>A synonymous_variant 0.94
clpC1 4040517 p.Val63Ala missense_variant 0.92
embC 4240671 p.Thr270Ile missense_variant 0.92
embC 4241042 p.Asn394Asp missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.99
embA 4245166 p.Pro645Gln missense_variant 0.97
embA 4245969 p.Pro913Ser missense_variant 0.96
embB 4247646 p.Glu378Ala missense_variant 0.89
ubiA 4269387 p.Glu149Asp missense_variant 0.91
aftB 4269411 c.-575T>C upstream_gene_variant 0.11
aftB 4269606 c.-770T>C upstream_gene_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.97
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4407873 c.330G>T synonymous_variant 0.93