TB-Profiler result

Run: ERR176630

Summary

Run ID: ERR176630

Sample name:

Date: 20-10-2023 22:22:15

Number of reads: 2497848

Percentage reads mapped: 95.47

Strain: lineage1.1.3.2

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 (0.15)
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
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.2 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.15 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 8188 p.Leu296Pro missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.98
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9445 p.Asn715Ser missense_variant 0.97
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619695 c.-196G>A upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.99
rpoC 763886 c.517C>A synonymous_variant 0.98
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801166 p.Gly120Ser missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.13
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.13
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.16
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.17
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.13
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.12
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.12
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.16
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.16
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.14
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.13
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.13
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.16
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.17
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.18
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.19
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.23
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.32
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.32
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.32
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.34
inhA 1674883 p.Ile228Val missense_variant 1.0
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 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 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.99
folC 2746207 c.1392C>T synonymous_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065448 c.744C>T synonymous_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
fbiB 3642173 c.639G>A synonymous_variant 1.0
rpoA 3878687 c.-180A>C upstream_gene_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.98
embA 4242418 c.-815C>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_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
whiB6 4338568 c.-47G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.99
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0