TB-Profiler result

Run: ERR4821453
Summary

Run ID: ERR4821453

Sample name:

Date: 01-04-2023 17:15:46

Number of reads: 778606

Percentage reads mapped: 99.82

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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
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 5684 p.Val149Phe missense_variant 0.2
gyrB 6408 p.Glu390Val missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8563 p.Leu421Pro missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490822 p.Gln14Lys missense_variant 0.13
rpoB 760675 p.Leu290Ser missense_variant 0.11
rpoB 761489 p.Glu561Asp missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417207 p.Asn47Lys missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673191 c.-249C>G upstream_gene_variant 0.12
fabG1 1673964 p.Asn175Lys missense_variant 0.15
rpsA 1834457 p.Pro306Thr missense_variant 0.12
rpsA 1834761 p.Phe407Tyr missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102276 p.Gly256Asp missense_variant 0.13
ndh 2103047 c.-5G>A upstream_gene_variant 0.11
katG 2155389 c.723C>G synonymous_variant 1.0
PPE35 2168938 p.Ser559Cys missense_variant 0.67
Rv1979c 2221723 p.Arg481Leu missense_variant 0.22
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.83
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519226 p.Leu371Pro missense_variant 0.25
ahpC 2726004 c.-189G>C upstream_gene_variant 0.15
folC 2746229 p.Ala457Asp missense_variant 0.11
pepQ 2859996 c.423G>A synonymous_variant 0.15
pepQ 2860346 p.Ser25Gly missense_variant 0.12
pepQ 2860551 c.-133C>T upstream_gene_variant 0.13
ribD 2987330 c.492G>A synonymous_variant 0.15
Rv2752c 3064717 p.Leu492Gln missense_variant 0.13
Rv2752c 3064784 p.Ser470Pro missense_variant 0.11
Rv2752c 3065019 c.1173C>T synonymous_variant 0.18
thyX 3067393 p.Val185Leu missense_variant 0.15
thyX 3067474 p.Pro158Ala missense_variant 1.0
ald 3087009 p.Val64Leu missense_variant 0.12
Rv3083 3448567 p.His22Asp missense_variant 1.0
Rv3083 3448630 p.Gly43Ser missense_variant 0.12
Rv3083 3449087 p.Ala195Val missense_variant 0.18
fprA 3473998 c.-9G>A upstream_gene_variant 1.0
fprA 3473998 c.-10_-9insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612910 p.Leu69Phe missense_variant 1.0
alr 3841379 c.42G>A synonymous_variant 0.12
ddn 3987158 p.Glu105Asp missense_variant 0.11
clpC1 4040644 p.Arg21Gly missense_variant 0.11
panD 4043901 c.380delA frameshift_variant 0.25
embC 4240466 p.Thr202Pro missense_variant 0.11
embC 4241963 p.Ala701Ser missense_variant 0.17
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4268617 p.Gly74Arg missense_variant 0.2
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0