TB-Profiler result

Run: ERR245821
Summary

Run ID: ERR245821

Sample name:

Date: 31-03-2023 18:22:57

Number of reads: 2226666

Percentage reads mapped: 99.6

Strain: lineage4.3.4.2.1

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
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
ethA 4327054 p.Tyr140* stop_gained 0.21 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
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7799 c.498A>C synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9435 p.Leu712Val missense_variant 0.21
ccsA 620407 p.Pro173Ala missense_variant 0.22
rpoB 762249 p.Leu815Val missense_variant 0.19
rpoC 762836 c.-534C>G upstream_gene_variant 0.2
rpoC 762839 c.-531G>A upstream_gene_variant 0.29
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765082 c.1713G>C synonymous_variant 0.44
rpoC 765234 p.Ala622Gly missense_variant 0.15
rpoC 766361 p.Val998Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416445 p.Tyr301* stop_gained 0.22
embR 1417136 p.Ser71Ile missense_variant 0.38
embR 1417501 c.-154A>C upstream_gene_variant 0.23
atpE 1461019 c.-26C>A upstream_gene_variant 0.21
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.25
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.24
fabG1 1673449 p.Thr4Pro missense_variant 0.26
inhA 1674334 p.Arg45Gly missense_variant 0.18
rpsA 1834631 p.Gln364Lys missense_variant 0.32
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154036 p.Ser692Arg missense_variant 0.26
PPE35 2169866 c.747G>C synonymous_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.2
eis 2715586 c.-254G>C upstream_gene_variant 0.75
ahpC 2725954 c.-239C>T upstream_gene_variant 0.29
ahpC 2726756 c.564C>G synonymous_variant 0.24
folC 2746186 c.1413G>C synonymous_variant 0.22
pepQ 2859381 c.1038C>G synonymous_variant 0.25
pepQ 2859680 p.Leu247Val missense_variant 0.15
pepQ 2859832 p.Ala196Gly missense_variant 0.31
pepQ 2859974 p.Ala149Pro missense_variant 0.25
Rv2752c 3064741 p.Gly484Ala missense_variant 0.75
thyA 3073800 c.672G>C synonymous_variant 0.24
thyA 3073817 p.Gln219Glu missense_variant 0.5
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449673 p.Tyr390* stop_gained 0.26
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475280 p.Val425Gly missense_variant 0.33
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.18
fbiB 3642734 c.1200G>C synonymous_variant 0.25
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3877766 p.Ala248Pro missense_variant 0.29
ddn 3987013 p.Gly57Ala missense_variant 0.23
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.25
clpC1 4039932 p.Gly258Val missense_variant 0.28
clpC1 4040233 p.Arg158Ser missense_variant 0.4
panD 4043938 p.Ile115Thr missense_variant 1.0
embC 4241429 p.Phe523Val missense_variant 0.46
embC 4241456 p.Ala532Pro missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.37
embC 4242827 p.Leu989Val missense_variant 0.27
embA 4244460 p.Val410Leu missense_variant 0.25
embB 4245713 c.-801G>C upstream_gene_variant 0.27
embB 4248725 p.Ser738Ala missense_variant 0.2
ubiA 4269529 p.Ala102Gly missense_variant 0.16
ethA 4327672 c.-199G>A upstream_gene_variant 0.25
whiB6 4338493 p.Thr10Lys missense_variant 0.36
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.98