TB-Profiler result

Run: ERR2245334
Summary

Run ID: ERR2245334

Sample name:

Date: 31-03-2023 17:38:13

Number of reads: 822027

Percentage reads mapped: 99.41

Strain: lineage3.1.1

Drug-resistance: Sensitive

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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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.99
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
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 5386 c.147G>T synonymous_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 0.94
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490747 c.-36C>G upstream_gene_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.33
rpoB 759691 c.-116A>G upstream_gene_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760835 p.His343Gln missense_variant 0.14
rpoB 761084 c.1278C>A synonymous_variant 0.22
rpoB 762433 p.Gly876Val missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766085 p.Pro906Ser missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776171 c.2310C>T synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800670 c.-139C>A upstream_gene_variant 0.22
fbiC 1303133 p.Ala68Glu missense_variant 0.12
fbiC 1303666 p.Thr246Pro missense_variant 0.15
Rv1258c 1407170 p.Phe57Leu missense_variant 0.15
Rv1258c 1407222 p.Ser40Ile missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673286 c.-154A>T upstream_gene_variant 0.13
inhA 1673448 c.-754C>G upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102377 c.666A>G synonymous_variant 0.12
ndh 2102382 c.661C>T synonymous_variant 0.13
ndh 2102389 c.654G>C synonymous_variant 0.14
ndh 2102392 c.651C>A synonymous_variant 0.15
ndh 2102401 c.642T>C synonymous_variant 0.17
ndh 2102407 c.636T>C synonymous_variant 0.15
ndh 2103010 c.33A>C synonymous_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154830 p.Gly428Trp missense_variant 0.2
katG 2155891 p.Asp74Ala missense_variant 0.2
katG 2156030 p.Tyr28His missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168823 p.Pro597Leu missense_variant 0.22
PPE35 2169049 p.Ile522Phe missense_variant 0.33
PPE35 2169056 c.1557A>T synonymous_variant 0.26
PPE35 2169144 p.Val490Glu missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.37
PPE35 2170053 p.Thr187Ser missense_variant 0.35
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2222899 p.Arg89Leu missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289763 c.-523delT upstream_gene_variant 0.2
eis 2714289 p.Glu348Asp missense_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726431 p.Ala80Asp missense_variant 0.14
folC 2746830 p.Ala257Pro missense_variant 0.18
folC 2746955 p.Glu215Val missense_variant 0.33
pepQ 2859627 p.Leu264Phe missense_variant 0.18
pepQ 2860255 p.Ala55Val missense_variant 0.17
Rv2752c 3064566 c.1626G>C synonymous_variant 0.44
Rv2752c 3065363 p.Gly277Cys missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339753 c.636A>G synonymous_variant 0.17
Rv3083 3448431 c.-73T>C upstream_gene_variant 0.13
Rv3083 3448964 p.Pro154His missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612412 c.705G>A synonymous_variant 0.33
alr 3840984 p.Arg146Leu missense_variant 0.12
clpC1 4038404 c.2301G>T synonymous_variant 0.12
clpC1 4039003 p.Asn568Asp missense_variant 0.33
clpC1 4039121 c.1584T>G synonymous_variant 0.2
clpC1 4039738 p.Thr323Pro missense_variant 0.25
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244497 p.Ala422Val missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.15
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4249669 p.Tyr1052* stop_gained 0.17
aftB 4268722 p.Arg39Cys missense_variant 0.12
ethA 4326074 p.Leu467Arg missense_variant 0.5
ethA 4326827 p.Pro216Gln missense_variant 0.12
ethA 4326860 p.Leu205Pro missense_variant 0.12
whiB6 4338474 p.Trp16Cys missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0