TB-Profiler result

Run: ERR245819
Summary

Run ID: ERR245819

Sample name:

Date: 31-03-2023 18:22:52

Number of reads: 1691222

Percentage reads mapped: 99.16

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 0.99
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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8445 p.Arg382Gly missense_variant 0.3
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.22
ccsA 620407 p.Pro173Ala missense_variant 0.27
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761285 c.1479G>C synonymous_variant 0.21
rpoB 762249 p.Leu815Val missense_variant 0.33
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.57
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoC 764725 p.Phe452Leu missense_variant 0.29
rpoC 766535 p.Glu1056Gln missense_variant 0.33
rpoC 767305 p.Tyr1312* stop_gained 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417233 c.115C>T synonymous_variant 0.31
embR 1417501 c.-154A>C upstream_gene_variant 0.37
rrs 1471658 n.-188T>G upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.16
inhA 1674892 p.Asn231Asp missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918069 p.Thr44Pro missense_variant 0.5
ndh 2101716 p.Glu443Gln missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155701 p.Asp137Glu missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.25
PPE35 2169986 p.Leu209Phe missense_variant 0.2
PPE35 2170461 p.Gly51Glu missense_variant 1.0
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
ahpC 2725954 c.-239C>T upstream_gene_variant 0.5
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726756 c.564C>G synonymous_variant 0.21
folC 2746186 c.1413G>C synonymous_variant 0.33
folC 2746608 p.Ala331Pro missense_variant 0.4
pepQ 2859381 c.1038C>G synonymous_variant 0.36
pepQ 2859680 p.Leu247Val missense_variant 0.25
pepQ 2859787 p.Val211Ala missense_variant 1.0
pepQ 2859920 p.Arg167Gly missense_variant 0.29
Rv2752c 3064552 p.Arg547Pro missense_variant 0.33
Rv2752c 3065265 c.927C>G synonymous_variant 0.31
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087811 p.Ala331Gly missense_variant 0.33
Rv3083 3449058 p.Ser185Arg missense_variant 0.55
Rv3083 3449673 p.Tyr390* stop_gained 0.37
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612425 p.Ala231Gly missense_variant 0.45
fbiB 3641955 p.Gly141Arg missense_variant 0.29
fbiB 3642734 c.1200G>C synonymous_variant 0.4
alr 3840494 c.927G>C synonymous_variant 0.25
alr 3841195 p.Arg76Gly missense_variant 0.15
clpC1 4038857 c.1848C>A synonymous_variant 0.23
clpC1 4039932 p.Gly258Val missense_variant 0.19
embC 4240355 p.Ala165Pro missense_variant 0.29
embC 4240646 p.Phe262Val missense_variant 0.33
embC 4241056 c.1194C>G synonymous_variant 0.3
embC 4241128 c.1266G>C synonymous_variant 0.4
embC 4241429 p.Phe523Val missense_variant 0.43
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 4242802 c.-431G>C upstream_gene_variant 0.2
embC 4242822 p.Val987Gly missense_variant 0.38
embA 4243977 p.Ala249Pro missense_variant 0.38
embA 4244375 c.1143C>G synonymous_variant 0.57
embA 4244460 p.Val410Leu missense_variant 0.38
embB 4246798 c.285C>G synonymous_variant 0.5
embB 4248725 p.Ser738Ala missense_variant 0.33
aftB 4267409 c.1428C>A synonymous_variant 0.22
ubiA 4269529 p.Ala102Gly missense_variant 0.31
ethA 4327672 c.-199G>A upstream_gene_variant 0.6
ethR 4327912 p.Arg122Gly missense_variant 0.4
whiB6 4338493 p.Thr10Lys missense_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0