TB-Profiler result

Run: ERR4820537
Summary

Run ID: ERR4820537

Sample name:

Date: 01-04-2023 16:44:25

Number of reads: 2942392

Percentage reads mapped: 94.35

Strain: lineage1.2.2.2

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
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
lineage1.2.2.2 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 7268 c.-34C>T upstream_gene_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 8668 p.Ala456Val 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
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
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.22
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.29
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.8
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.75
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.5
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.75
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.5
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.75
rrs 1472263 n.418C>T non_coding_transcript_exon_variant 0.5
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.67
rrs 1472279 n.434T>A non_coding_transcript_exon_variant 0.67
rrs 1472514 n.669T>C non_coding_transcript_exon_variant 1.0
rrs 1472712 n.867G>A non_coding_transcript_exon_variant 0.75
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.75
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.75
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.6
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.67
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.67
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.67
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.2
rrl 1476128 n.2471T>A non_coding_transcript_exon_variant 0.5
rrl 1476422 n.2765C>G non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.6
rrl 1476638 n.2981C>A non_coding_transcript_exon_variant 0.15
rrl 1476706 n.3049C>T non_coding_transcript_exon_variant 0.17
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 2168742 p.Gly624Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222398 p.Ile256Thr 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 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
rpoA 3878656 c.-149C>A upstream_gene_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_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 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268323 p.Leu172Phe missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys 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 4407742 p.Arg154Pro missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0