TB-Profiler result

Run: ERR4423486
Summary

Run ID: ERR4423486

Sample name:

Date: 01-04-2023 05:50:56

Number of reads: 738849

Percentage reads mapped: 99.22

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 0.99
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
rpoB 761140 p.His445Leu missense_variant 1.0 rifampicin
katG 2154642 c.1469delG frameshift_variant 0.14 isoniazid
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 8114 c.813C>A synonymous_variant 0.19
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490960 p.Ala60Ser missense_variant 0.14
fgd1 491192 p.Gly137Val missense_variant 0.13
fgd1 491408 p.Pro209Gln missense_variant 0.17
fgd1 491691 p.Trp303Cys missense_variant 0.14
rpoB 761709 p.Val635Phe missense_variant 0.2
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
fbiC 1304258 p.Ser443Tyr missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673393 c.-809G>C upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102361 p.Leu228Ile missense_variant 0.14
katG 2154296 p.Ala606Ser missense_variant 0.12
katG 2155005 c.1107C>A synonymous_variant 0.15
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067261 p.Asp229Tyr missense_variant 0.18
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568639 p.Arg14Ile missense_variant 0.12
rpoA 3878394 c.114G>T synonymous_variant 0.25
ddn 3987011 c.168C>T synonymous_variant 1.0
embC 4241502 p.Ser547* stop_gained 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244840 c.1608G>A synonymous_variant 0.2
embA 4245317 c.2085G>T synonymous_variant 0.17
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4268605 p.Arg78Ser missense_variant 0.15
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338440 p.Glu28Lys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0