TB-Profiler result

Run: ERR4828628

Summary

Run ID: ERR4828628

Sample name:

Date: 01-04-2023 18:59:40

Number of reads: 1141642

Percentage reads mapped: 88.74

Strain: lineage4.5

Drug-resistance: MDR-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
lineage4.5 Euro-American H;T RD122 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
rpoB 761098 p.Ser431Thr missense_variant 0.1 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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 6256 c.1017G>A synonymous_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.22
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoB 759652 c.-155G>A upstream_gene_variant 0.13
rpoB 760181 c.375T>G synonymous_variant 0.15
rpoB 760184 c.378A>G synonymous_variant 0.15
rpoB 760223 c.417T>C synonymous_variant 0.15
rpoB 760233 c.427_429delAGTinsTCG synonymous_variant 0.15
rpoB 760241 c.435G>C synonymous_variant 0.15
rpoB 760244 c.438G>C synonymous_variant 0.14
rpoB 760253 c.447T>C synonymous_variant 0.14
rpoB 760256 c.450C>T synonymous_variant 0.13
rpoB 760262 c.456G>C synonymous_variant 0.13
rpoB 760271 c.465C>G synonymous_variant 0.13
rpoB 760274 p.Glu156Asp missense_variant 0.14
rpoB 760436 c.630C>G synonymous_variant 0.12
rpoB 760475 c.669A>G synonymous_variant 0.1
rpoB 760508 c.702G>C synonymous_variant 0.15
rpoB 760511 c.705G>C synonymous_variant 0.14
rpoB 760514 c.708C>T synonymous_variant 0.14
rpoB 760591 p.Val262Ala missense_variant 0.15
rpoB 760611 c.805_807delTTGinsCTC synonymous_variant 0.19
rpoB 760634 c.828T>C synonymous_variant 0.19
rpoB 760646 c.840C>G synonymous_variant 0.12
rpoB 760649 c.843G>C synonymous_variant 0.12
rpoB 760652 c.846C>G synonymous_variant 0.11
rpoB 760679 c.873A>G synonymous_variant 0.1
rpoB 761088 c.1282_1284delAGCinsTCG synonymous_variant 0.11
rpoB 761102 c.1296A>G synonymous_variant 0.11
rpoB 761999 c.2193G>C synonymous_variant 0.1
rpoB 762002 c.2196C>G synonymous_variant 0.1
rpoB 762003 p.Asn733His missense_variant 0.1
rpoB 762143 c.2337T>C synonymous_variant 0.1
rpoB 762176 c.2370T>C synonymous_variant 0.1
rpoB 762185 c.2379G>C synonymous_variant 0.1
rpoC 763699 c.330G>C synonymous_variant 0.12
rpoC 763702 c.333C>G synonymous_variant 0.12
rpoC 763708 c.339G>C synonymous_variant 0.12
rpoC 763711 c.342G>C synonymous_variant 0.11
rpoC 763717 c.348T>C synonymous_variant 0.11
rpoC 763732 c.363C>G synonymous_variant 0.12
rpoC 763735 c.366G>C synonymous_variant 0.12
rpoC 763741 c.372C>T synonymous_variant 0.12
rpoC 763744 c.375G>C synonymous_variant 0.11
rpoC 764764 c.1395T>C synonymous_variant 0.11
rpoC 764782 p.Ser471Arg missense_variant 0.1
rpoC 764797 c.1428G>C synonymous_variant 0.11
rpoC 764803 c.1434C>G synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781829 c.270G>C synonymous_variant 0.1
rpsL 781832 c.273T>G synonymous_variant 0.11
rpsL 781838 c.279G>T synonymous_variant 0.11
rpsL 781892 c.333A>G synonymous_variant 0.14
rpsL 781898 c.339A>G synonymous_variant 0.16
rplC 800830 p.Gly8Ser missense_variant 0.14
atpE 1460947 c.-98C>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.2
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.14
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.14
rrl 1473651 n.-7G>A upstream_gene_variant 0.11
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.22
rrl 1476740 n.3083G>T non_coding_transcript_exon_variant 0.14
rpsA 1833928 c.387G>C synonymous_variant 0.11
rpsA 1833940 c.399C>G synonymous_variant 0.11
rpsA 1833952 c.411C>T synonymous_variant 0.12
rpsA 1833955 c.414G>C synonymous_variant 0.12
rpsA 1833961 c.420C>G synonymous_variant 0.12
rpsA 1833970 c.429G>C synonymous_variant 0.11
rpsA 1833973 c.432G>C synonymous_variant 0.1
rpsA 1833979 c.438T>C synonymous_variant 0.11
rpsA 1833985 c.444G>C synonymous_variant 0.1
rpsA 1834012 c.471G>C synonymous_variant 0.1
rpsA 1834354 c.813G>C synonymous_variant 0.11
rpsA 1834357 c.816T>C synonymous_variant 0.12
rpsA 1834361 c.820T>C synonymous_variant 0.11
rpsA 1834366 c.825A>G synonymous_variant 0.12
rpsA 1834384 c.843A>G synonymous_variant 0.11
rpsA 1834387 c.846C>T synonymous_variant 0.11
rpsA 1834399 p.His286Gln missense_variant 0.12
rpsA 1834408 c.867C>G synonymous_variant 0.11
rpsA 1834417 c.876G>C synonymous_variant 0.11
rpsA 1834423 c.882G>C synonymous_variant 0.16
rpsA 1834435 c.894G>C synonymous_variant 0.16
rpsA 1834451 c.910_912delTTGinsCTC synonymous_variant 0.11
rpsA 1834456 c.915T>C synonymous_variant 0.11
rpsA 1834465 c.924T>C synonymous_variant 0.11
rpsA 1834468 c.927A>G synonymous_variant 0.11
rpsA 1834486 p.Glu315Asp missense_variant 0.12
rpsA 1834489 c.948T>C synonymous_variant 0.14
rpsA 1834501 c.960G>C synonymous_variant 0.11
rpsA 1834504 c.963G>C synonymous_variant 0.11
rpsA 1834513 c.972C>G synonymous_variant 0.11
rpsA 1834528 c.987T>C synonymous_variant 0.11
rpsA 1834733 p.Ala398Pro missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918232 p.Glu98Val missense_variant 1.0
PPE35 2168647 p.Val656Met missense_variant 0.13
PPE35 2169063 p.Met517Lys missense_variant 0.14
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289118 p.His42Tyr missense_variant 1.0
ahpC 2726230 p.Tyr13Cys missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877686 c.822A>G synonymous_variant 0.11
rpoA 3877776 c.732T>C synonymous_variant 0.1
rpoA 3877782 c.726T>C synonymous_variant 0.15
rpoA 3877848 c.660C>G synonymous_variant 0.12
rpoA 3877856 c.652T>C synonymous_variant 0.15
rpoA 3877866 c.642G>C synonymous_variant 0.17
rpoA 3877875 c.633T>G synonymous_variant 0.18
rpoA 3877893 c.615C>G synonymous_variant 0.15
rpoA 3877898 p.Pro204Ala missense_variant 0.14
rpoA 3877900 p.Ser203Thr missense_variant 0.14
rpoA 3877902 p.Ile202Met missense_variant 0.14
rpoA 3877905 c.603A>G synonymous_variant 0.15
rpoA 3877908 c.600T>C synonymous_variant 0.16
rpoA 3877920 c.588G>C synonymous_variant 0.17
rpoA 3877935 p.Lys191Arg missense_variant 0.12
rpoA 3877962 c.546G>T synonymous_variant 0.17
rpoA 3877971 p.Asp179Glu missense_variant 0.1
rpoA 3877974 c.534G>C synonymous_variant 0.11
rpoA 3877989 c.519A>G synonymous_variant 0.14
rpoA 3877992 c.516C>G synonymous_variant 0.14
rpoA 3877998 c.510G>C synonymous_variant 0.1
rpoA 3878001 c.507A>G synonymous_variant 0.1
rpoA 3878127 c.381G>C synonymous_variant 0.12
rpoA 3878141 p.Met123Leu missense_variant 0.11
rpoA 3878154 c.354G>C synonymous_variant 0.11
rpoA 3878175 c.333G>C synonymous_variant 0.11
rpoA 3878187 c.321C>G synonymous_variant 0.18
rpoA 3878193 c.315T>C synonymous_variant 0.16
rpoA 3878196 p.Glu104Ala missense_variant 0.17
rpoA 3878199 c.309T>C synonymous_variant 0.19
rpoA 3878217 p.Leu97Val missense_variant 0.19
rpoA 3878241 p.Glu89Asp missense_variant 0.17
rpoA 3878250 c.258C>G synonymous_variant 0.18
rpoA 3878253 c.255G>C synonymous_variant 0.18
rpoA 3878256 c.252G>C synonymous_variant 0.19
rpoA 3878264 p.Ser82Gly missense_variant 0.18
rpoA 3878271 c.237T>C synonymous_variant 0.17
rpoA 3878283 p.Glu75Asp missense_variant 0.11
rpoA 3878295 c.213A>G synonymous_variant 0.12
rpoA 3878298 c.210A>G synonymous_variant 0.11
rpoA 3878301 c.207C>G synonymous_variant 0.11
rpoA 3878304 c.204G>C synonymous_variant 0.11
rpoA 3878310 c.198G>C synonymous_variant 0.11
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
clpC1 4038899 c.1806C>G synonymous_variant 0.11
clpC1 4038905 c.1800A>G synonymous_variant 0.12
clpC1 4038914 c.1791G>C synonymous_variant 0.12
clpC1 4038917 c.1788C>T synonymous_variant 0.12
clpC1 4038923 c.1782A>G synonymous_variant 0.1
clpC1 4038926 c.1779G>C synonymous_variant 0.11
clpC1 4038932 c.1773G>C synonymous_variant 0.11
clpC1 4039004 c.1701C>G synonymous_variant 0.13
clpC1 4039766 c.939T>C synonymous_variant 0.1
clpC1 4039769 c.936C>G synonymous_variant 0.11
clpC1 4039778 c.927A>G synonymous_variant 0.11
clpC1 4039781 c.924G>C synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243640 c.408T>C synonymous_variant 1.0
ethR 4327027 c.-522C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0