TB-Profiler result

Run: ERR2229074
Summary

Run ID: ERR2229074

Sample name:

Date: 31-03-2023 16:35:41

Number of reads: 339658

Percentage reads mapped: 99.43

Strain: lineage4

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
lineage4 Euro-American LAM;T;S;X;H 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 2154695 c.1416delA frameshift_variant 0.2 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 5686 c.447T>C synonymous_variant 0.2
gyrB 6645 p.Ser469Asn missense_variant 0.25
gyrA 7150 c.-152G>T upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 490900 p.His40Asn missense_variant 0.18
fgd1 491149 p.Pro123Ser missense_variant 0.18
rpoC 764830 c.1461C>T synonymous_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406157 p.Ile395Thr missense_variant 0.25
embR 1416635 p.Asp238Val missense_variant 0.14
embR 1417425 c.-78C>T upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472509 n.664G>T non_coding_transcript_exon_variant 0.18
rrs 1472764 n.919G>T non_coding_transcript_exon_variant 0.29
rrs 1473263 n.1418A>G non_coding_transcript_exon_variant 0.25
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476010 n.2353G>A non_coding_transcript_exon_variant 0.2
fabG1 1673211 c.-229T>A upstream_gene_variant 0.25
rpsA 1833484 c.-58C>T upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155918 p.Ala65Val missense_variant 0.2
katG 2155997 p.Trp39Arg missense_variant 0.13
PPE35 2168059 p.Gln852* stop_gained 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169308 c.1305C>T synonymous_variant 0.17
PPE35 2169602 c.1011C>A synonymous_variant 0.2
PPE35 2169767 c.846A>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.29
Rv1979c 2221785 c.1380G>A synonymous_variant 0.12
Rv1979c 2222008 p.Phe386Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518879 c.765A>G synonymous_variant 0.25
kasA 2518882 c.768C>A synonymous_variant 0.25
Rv2752c 3064534 p.Pro553Gln missense_variant 0.33
Rv2752c 3064667 p.Arg509Ser missense_variant 0.33
alr 3840953 c.468C>A synonymous_variant 0.2
rpoA 3878311 p.Val66Ala missense_variant 0.15
ddn 3987221 p.Leu126Phe missense_variant 0.2
panD 4044060 c.222C>G synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243087 c.-146G>A upstream_gene_variant 0.2
embA 4243280 c.48A>G synonymous_variant 0.12
embA 4244184 p.Ser318Leu missense_variant 0.5
embA 4244286 p.Gly352Cys missense_variant 0.33
embA 4244737 p.Tyr502Phe missense_variant 0.5
embA 4245176 c.1944G>A synonymous_variant 0.18
embB 4249199 p.Gln896Lys missense_variant 0.22
ubiA 4269788 p.Gly16Arg missense_variant 0.15
ethA 4326954 p.Asp174Asn missense_variant 0.17
ethR 4326961 c.-588G>C upstream_gene_variant 0.14
ethR 4326964 c.-585G>A upstream_gene_variant 0.15
ethR 4326970 c.-579G>T upstream_gene_variant 0.17
whiB6 4338471 p.Arg17Ser missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0