TB-Profiler result

Run: ERR245725
Summary

Run ID: ERR245725

Sample name:

Date: 31-03-2023 18:17:28

Number of reads: 13997591

Percentage reads mapped: 99.55

Strain: lineage4.3.4.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 2155841 p.Trp91Arg missense_variant 0.11 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 6140 p.Val301Leu missense_variant 1.0
gyrB 6934 p.Gln565His missense_variant 0.28
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.19
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.19
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767305 p.Tyr1312* stop_gained 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407522 c.-182C>G upstream_gene_variant 0.29
atpE 1461019 c.-26C>A upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.17
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.21
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155337 p.Asp259Tyr missense_variant 0.86
PPE35 2169866 c.747G>C synonymous_variant 0.24
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.25
eis 2714569 p.Ala255Gly missense_variant 0.18
eis 2715586 c.-254G>C upstream_gene_variant 0.29
ahpC 2725954 c.-239C>T upstream_gene_variant 0.3
folC 2746186 c.1413G>C synonymous_variant 0.21
Rv2752c 3064741 p.Gly484Ala missense_variant 0.22
thyA 3073817 p.Gln219Glu missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.23
Rv3083 3449673 p.Tyr390* stop_gained 0.19
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.25
fbiB 3642734 c.1200G>C synonymous_variant 0.24
alr 3840719 c.702A>G synonymous_variant 1.0
ddn 3987013 p.Gly57Ala missense_variant 0.19
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039932 p.Gly258Val missense_variant 0.26
embC 4239870 p.Thr3Asn missense_variant 0.2
embC 4241056 c.1194C>G synonymous_variant 0.3
embC 4241429 p.Phe523Val missense_variant 0.35
embC 4242476 p.Pro872Ala missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.32
embA 4243190 c.-43G>C upstream_gene_variant 0.15
embA 4244375 c.1143C>G synonymous_variant 0.24
ubiA 4269529 p.Ala102Gly missense_variant 0.25
ethA 4327672 c.-199G>A upstream_gene_variant 0.24
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0