TB-Profiler result

Run: ERR11050167
Summary

Run ID: ERR11050167

Sample name:

Date: 02-04-2023 14:31:47

Number of reads: 450857

Percentage reads mapped: 99.69

Strain: lineage4.4.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T 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
ethA 4326419 c.1054delG 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
gyrB 5633 p.Ser132Thr missense_variant 0.15
gyrB 6896 p.Arg553Trp missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8041 p.Gly247Ala missense_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576119 p.Ala258Pro missense_variant 0.5
mshA 576606 p.Ala420Gly missense_variant 0.67
rpoB 760923 p.Arg373Cys missense_variant 0.14
rpoC 764065 c.696G>A synonymous_variant 0.13
rpoC 764367 p.Gly333Ala missense_variant 0.33
rpoC 766195 c.2826A>G synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777127 p.Ser452Arg missense_variant 0.25
mmpL5 777883 p.Gly200Arg missense_variant 0.29
mmpS5 778627 p.Lys93Asn missense_variant 0.5
mmpL5 778982 c.-502A>T upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304252 p.Val441Ala missense_variant 0.29
Rv1258c 1407015 p.Leu109Trp missense_variant 0.22
Rv1258c 1407061 p.Trp94Gly missense_variant 0.33
embR 1416430 c.918G>C synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.24
rrl 1476160 n.2507delA non_coding_transcript_exon_variant 0.2
fabG1 1674112 p.Ala225Thr missense_variant 0.25
inhA 1674273 c.72C>T synonymous_variant 0.2
inhA 1674399 p.Gln66His missense_variant 0.29
rpsA 1834959 p.Leu473Arg missense_variant 0.25
tlyA 1918116 p.Glu59Asp missense_variant 0.67
ndh 2102297 p.Val249Asp missense_variant 0.25
ndh 2102990 p.Val18Ala missense_variant 1.0
ndh 2103121 c.-79G>A upstream_gene_variant 0.12
PPE35 2169391 p.Asn408Asp missense_variant 0.25
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170075 p.Ala180Pro missense_variant 0.5
Rv1979c 2221935 p.Asn410Lys missense_variant 0.11
Rv1979c 2221980 c.1185A>G synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289786 c.-545G>C upstream_gene_variant 0.33
folC 2746377 p.Ser408Ala missense_variant 0.2
folC 2747096 p.Val168Gly missense_variant 0.19
pepQ 2859933 c.486C>G synonymous_variant 0.4
pepQ 2860144 p.Val92Gly missense_variant 0.5
pepQ 2860266 c.153T>C synonymous_variant 0.11
thyX 3067963 c.-18G>C upstream_gene_variant 0.29
thyA 3074438 p.Leu12Phe missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087111 p.Ala98Thr missense_variant 0.18
ald 3087816 p.Cys333Gly missense_variant 0.2
fbiD 3339315 p.Glu66Asp missense_variant 0.25
fbiD 3339751 p.Ala212Pro missense_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473977 c.-30C>T upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475121 p.Lys372Arg missense_variant 0.25
whiB7 3568486 p.Val65Gly missense_variant 0.17
Rv3236c 3612614 p.Leu168Arg missense_variant 0.25
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiA 3641026 p.Glu162Gln missense_variant 0.17
alr 3840357 p.Leu355Arg missense_variant 0.4
rpoA 3877822 p.Ala229Val missense_variant 0.22
clpC1 4039800 p.Ile302Asn missense_variant 0.25
clpC1 4040235 p.Gly157Ala missense_variant 0.17
clpC1 4040545 p.Ile54Phe missense_variant 0.25
clpC1 4040550 p.Leu52Trp missense_variant 0.33
embC 4239667 c.-196C>T upstream_gene_variant 0.29
embC 4239708 c.-155A>T upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243198 c.-35A>C upstream_gene_variant 0.33
embA 4243214 c.-19T>G upstream_gene_variant 0.33
embB 4246181 c.-333C>T upstream_gene_variant 0.2
embB 4246472 c.-42T>A upstream_gene_variant 0.4
embB 4246527 p.Ala5Gly missense_variant 1.0
embB 4248131 p.Arg540Gly missense_variant 0.18
embB 4249493 p.Phe994Val missense_variant 0.22
ubiA 4269496 p.Ser113Leu missense_variant 0.2
ubiA 4269563 p.Pro91Ser missense_variant 0.29
whiB6 4338200 p.Asp108His missense_variant 0.43
whiB6 4338205 p.Val106Gly missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407612 c.591T>C synonymous_variant 0.33