TB-Profiler result

Run: ERR4816828

Summary

Run ID: ERR4816828

Sample name:

Date: 20-10-2023 08:13:02

Number of reads: 4449332

Percentage reads mapped: 96.4

Strain: lineage1.1.1

Drug-resistance: Other


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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 R rrs n.888G>A (0.90)
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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.1 Indo-Oceanic EAI4;EAI5 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.9 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 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 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761770 p.Met655Thr 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
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776567 p.Met638Ile missense_variant 1.0
mmpL5 777432 p.Ala350Gly missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.77
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.87
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.96
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.96
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.92
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.15
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.93
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.97
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.97
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.78
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.78
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.89
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.89
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.85
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.81
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.81
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.81
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.36
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.4
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.36
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.47
rpsA 1834319 p.Val260Ile missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103022 c.21C>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 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223144 p.Arg7Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518123 c.9G>A synonymous_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473812 c.-195G>A upstream_gene_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 0.99
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267339 p.Leu500Phe missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338242 p.Gln94Glu missense_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
gid 4408345 c.-143C>T upstream_gene_variant 1.0