TB-Profiler result

Run: ERR4813641

Summary

Run ID: ERR4813641

Sample name:

Date: 01-04-2023 12:53:44

Number of reads: 636023

Percentage reads mapped: 97.98

Strain: lineage4

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
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
gid 4407851 c.351dupG frameshift_variant 1.0 streptomycin
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 5057 c.-183G>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8727 p.Arg476Cys missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575229 c.-119T>C upstream_gene_variant 0.33
mshA 575404 c.57C>A synonymous_variant 0.4
mshA 576108 p.Ala254Gly missense_variant 0.25
ccsA 619789 c.-102G>T upstream_gene_variant 0.22
ccsA 620505 c.615G>A synonymous_variant 0.13
rpoB 761659 p.Pro618Gln missense_variant 0.15
rpoB 761889 p.Val695Leu missense_variant 1.0
rpoB 762130 p.Leu775Pro missense_variant 0.11
rpoB 762149 c.2343G>T synonymous_variant 0.15
rpoB 763260 p.Ala1152Ser missense_variant 0.22
rpoC 765922 c.2553C>A synonymous_variant 0.18
rpoC 765981 p.Gly871Asp missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779163 c.-683C>A upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781580 c.21G>A synonymous_variant 0.15
rplC 801009 c.201A>G synonymous_variant 1.0
fbiC 1303167 c.237C>T synonymous_variant 0.13
fbiC 1303424 p.Arg165Leu missense_variant 0.15
Rv1258c 1407466 c.-126G>T upstream_gene_variant 0.29
embR 1416743 p.Pro202His missense_variant 0.13
embR 1416941 p.Arg136Leu missense_variant 0.12
rrs 1471655 n.-191G>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476117 n.2460G>T non_coding_transcript_exon_variant 0.15
rrl 1476205 n.2548A>G non_coding_transcript_exon_variant 0.12
inhA 1674377 p.Pro59Gln missense_variant 0.18
rpsA 1833372 c.-170C>T upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918739 p.Gly267Asp missense_variant 1.0
ndh 2102614 c.429C>T synonymous_variant 0.14
Rv1979c 2223138 c.27T>C synonymous_variant 0.12
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714512 p.Pro274Gln missense_variant 0.13
ahpC 2726303 c.111T>C synonymous_variant 0.14
folC 2747174 p.Ala142Val missense_variant 0.17
Rv2752c 3065032 p.Gly387Val missense_variant 0.11
Rv2752c 3065517 c.675C>T synonymous_variant 1.0
thyA 3074310 c.162G>T synonymous_variant 0.12
Rv3083 3448439 c.-64delA upstream_gene_variant 1.0
Rv3083 3449933 p.Pro477Leu missense_variant 0.12
fprA 3474299 p.Asp98Gly missense_variant 1.0
fprA 3475163 p.Leu386His missense_variant 0.22
whiB7 3568401 c.279G>T stop_lost&splice_region_variant 0.38
Rv3236c 3612448 c.669G>T synonymous_variant 0.21
alr 3840285 p.Trp379Leu missense_variant 0.22
rpoA 3877543 p.Gly322Val missense_variant 0.12
rpoA 3878595 c.-88C>T upstream_gene_variant 0.33
clpC1 4038394 p.Arg771Ser missense_variant 0.12
clpC1 4040010 p.Ala232Asp missense_variant 0.11
clpC1 4040583 p.Gly41Val missense_variant 0.11
panD 4044371 c.-90G>T upstream_gene_variant 0.14
embC 4239781 c.-82C>A upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242801 p.Pro980Gln missense_variant 0.29
embA 4243129 c.-104G>A upstream_gene_variant 0.17
embA 4245146 p.Gln638His missense_variant 0.12
embA 4245466 p.Pro745Arg missense_variant 0.29
embA 4245733 p.Pro834Gln missense_variant 0.5
embA 4246460 p.Glu1076Asp missense_variant 0.15
embB 4247028 p.Leu172Arg missense_variant 0.27
embB 4248057 p.Ser515Thr missense_variant 0.14
embB 4249786 c.3273G>T synonymous_variant 0.13
aftB 4267786 p.Gly351Trp missense_variant 0.17
ubiA 4269709 p.Gly42Val missense_variant 0.12
ethR 4328110 p.Ala188Pro missense_variant 0.12
ethA 4328317 c.-844C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0