TB-Profiler result

Run: ERR4832040
Summary

Run ID: ERR4832040

Sample name:

Date: 01-04-2023 21:17:10

Number of reads: 901474

Percentage reads mapped: 99.73

Strain: lineage2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.1 East-Asian (non-Beijing) None None 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
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
ethA 4326166 c.1307delC frameshift_variant 1.0 ethionamide, ethionamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8848 p.Val516Ala missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575851 c.504C>T synonymous_variant 1.0
mshA 576318 p.Arg324Gln missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765121 c.1752G>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
fbiC 1304159 p.Val410Gly missense_variant 0.17
fbiC 1304443 p.Ala505Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472297 n.452G>T non_coding_transcript_exon_variant 0.5
rrs 1472795 n.950T>C non_coding_transcript_exon_variant 0.29
rrl 1474500 n.843T>C non_coding_transcript_exon_variant 0.4
rrl 1475587 n.1930G>T non_coding_transcript_exon_variant 0.5
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.16
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168696 c.1917C>T synonymous_variant 0.25
PPE35 2168955 p.Phe553Ser missense_variant 0.12
PPE35 2169673 p.Ser314Pro missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289898 c.-657C>T upstream_gene_variant 1.0
kasA 2518924 c.810C>A synonymous_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.23
ahpC 2726341 p.Val50Gly missense_variant 0.3
ahpC 2726350 p.Trp53Leu missense_variant 0.18
Rv2752c 3065616 c.576C>T synonymous_variant 1.0
thyA 3074645 c.-174T>G upstream_gene_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878489 p.Pro7Ser missense_variant 0.12
clpC1 4040841 c.-138delG upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243007 p.Leu1049Val missense_variant 1.0
embB 4246088 c.-426A>G upstream_gene_variant 1.0
embB 4246277 c.-237G>A upstream_gene_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408002 c.191_200delGGGTCGTGGA frameshift_variant 1.0