TB-Profiler result

Run: ERR4830536
Summary

Run ID: ERR4830536

Sample name:

Date: 01-04-2023 20:16:41

Number of reads: 388457

Percentage reads mapped: 99.37

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
gid 4408087 c.115delC 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 5793 p.Tyr185Cys missense_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7838 c.537C>T synonymous_variant 0.15
gyrA 7884 p.Arg195Cys missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9539 c.2238C>G synonymous_variant 0.12
fgd1 491428 p.Ala216Thr missense_variant 0.25
fgd1 491769 c.987A>T synonymous_variant 0.13
mshA 575306 c.-42T>C upstream_gene_variant 0.13
mshA 575369 p.Asp8Tyr missense_variant 0.12
mshA 575989 c.642C>T synonymous_variant 0.14
mshA 576207 p.Ala287Val missense_variant 0.17
ccsA 619966 p.Val26Leu missense_variant 0.13
ccsA 620283 c.393T>A synonymous_variant 0.14
ccsA 620405 p.Leu172Pro missense_variant 0.11
rpoB 760273 p.Glu156Gly missense_variant 0.11
rpoB 760471 p.Arg222His missense_variant 0.11
rpoB 760748 c.942C>G synonymous_variant 0.12
rpoB 760985 c.1179G>A synonymous_variant 0.12
rpoB 761429 c.1623G>A synonymous_variant 0.13
rpoB 761686 p.Arg627His missense_variant 0.14
rpoB 761915 c.2109C>T synonymous_variant 0.11
rpoB 762012 p.Val736Leu missense_variant 0.2
rpoB 762412 p.Gln869Pro missense_variant 0.2
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765463 p.Asn698Lys missense_variant 0.14
rpoC 765651 p.Gln761Arg missense_variant 0.11
rpoC 766824 p.Lys1152Thr missense_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777801 p.Ile227Thr missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rplC 801320 p.Gly171Asp missense_variant 0.12
fbiC 1303691 p.Pro254Leu missense_variant 0.13
fbiC 1303881 c.951G>C synonymous_variant 0.11
fbiC 1304468 p.Glu513Ala missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471778 n.-68G>A upstream_gene_variant 0.12
rrl 1473894 n.238_239delCC non_coding_transcript_exon_variant 0.11
inhA 1674018 c.-184G>A upstream_gene_variant 0.33
inhA 1674423 p.Leu74Phe missense_variant 0.2
rpsA 1833382 c.-160G>C upstream_gene_variant 0.14
rpsA 1834102 c.561T>A synonymous_variant 0.12
rpsA 1834144 p.Glu201Asp missense_variant 0.14
rpsA 1834176 p.Arg212Gln missense_variant 0.12
tlyA 1917767 c.-173T>C upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918326 c.387G>T synonymous_variant 0.25
ndh 2102391 p.Pro218Ser missense_variant 0.15
katG 2154715 p.Gly466Glu missense_variant 0.18
katG 2155177 p.Ala312Val missense_variant 0.2
katG 2155764 c.348C>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290200 c.-959A>C upstream_gene_variant 0.14
kasA 2518895 p.Pro261Ser missense_variant 0.25
folC 2746282 c.1317T>C synonymous_variant 0.12
folC 2747002 c.597T>A synonymous_variant 0.12
pepQ 2859588 c.831G>A synonymous_variant 0.2
pepQ 2860402 p.Arg6His missense_variant 0.12
pepQ 2860518 c.-100C>T upstream_gene_variant 0.18
ribD 2987511 p.Arg225Ser missense_variant 0.17
Rv2752c 3065150 p.Val348Phe missense_variant 0.11
Rv2752c 3066105 c.87C>A synonymous_variant 0.13
Rv2752c 3066183 c.9A>G synonymous_variant 0.13
Rv2752c 3066214 c.-23G>C upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087853 p.Thr345Arg missense_variant 0.11
fbiD 3339586 p.Ala157Pro missense_variant 0.18
Rv3083 3449327 p.Arg275Leu missense_variant 0.12
Rv3083 3449442 c.939G>A synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568780 c.-101A>G upstream_gene_variant 0.13
Rv3236c 3613213 c.-97C>A upstream_gene_variant 0.14
fbiA 3640737 p.Cys65* stop_gained 0.12
fbiB 3642373 p.Val280Asp missense_variant 0.25
fbiB 3642521 c.987C>T synonymous_variant 0.12
alr 3840218 c.1203C>A synonymous_variant 0.11
alr 3840385 p.Phe346Ile missense_variant 0.15
rpoA 3877669 p.Glu280Val missense_variant 0.12
rpoA 3877806 c.702C>T synonymous_variant 0.12
clpC1 4038185 c.2520G>A synonymous_variant 0.14
clpC1 4039071 p.Pro545Gln missense_variant 0.12
embC 4241038 c.1176G>A synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243890 p.Gly220Trp missense_variant 0.18
embA 4244160 p.Val310Met missense_variant 0.17
embA 4244883 p.Arg551Gly missense_variant 0.29
embA 4244909 c.1677C>T synonymous_variant 0.22
embB 4246899 p.Asn129Thr missense_variant 0.15
embB 4248692 p.Val727Leu missense_variant 0.15
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249436 p.Gln975* stop_gained 0.12
embB 4249473 p.Asp987Gly missense_variant 0.12
aftB 4267588 p.Ala417Thr missense_variant 0.17
aftB 4268065 p.Ser258Pro missense_variant 0.13
aftB 4268271 p.Phe189Ser missense_variant 0.17
aftB 4268964 c.-128G>A upstream_gene_variant 0.11
ubiA 4269126 p.Trp236* stop_gained 0.1
aftB 4269438 c.-602C>T upstream_gene_variant 0.12
ubiA 4269868 c.-35G>A upstream_gene_variant 0.14
ethA 4326108 p.Arg456Gly missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0