TB-Profiler result

Run: ERR9892674
Summary

Run ID: ERR9892674

Sample name:

Date: 02-04-2023 13:27:25

Number of reads: 873828

Percentage reads mapped: 98.82

Strain: lineage4.6.2.2

Drug-resistance: Other

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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
embC 4240751 p.Ile297Leu missense_variant 0.29 ethambutol
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 6704 p.Glu489Gln missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576245 p.Gly300* stop_gained 0.2
mshA 576636 p.Trp430Leu missense_variant 0.17
ccsA 619879 c.-12A>G upstream_gene_variant 0.18
ccsA 620283 c.393T>C synonymous_variant 0.2
ccsA 620804 p.Phe305Ser missense_variant 0.11
rpoB 761959 p.Met718Thr missense_variant 0.11
rpoC 764106 c.739delC frameshift_variant 0.11
rpoC 764212 c.844_847delCGAA frameshift_variant 0.13
rpoC 764480 p.Lys371Glu missense_variant 0.12
rpoC 766086 p.Pro906Leu missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776055 p.Val809Ala missense_variant 0.25
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781463 c.-97T>A upstream_gene_variant 0.11
rpsL 781478 c.-82C>T upstream_gene_variant 0.12
rplC 801400 p.Val198Phe missense_variant 0.13
rplC 801432 c.624C>A synonymous_variant 0.12
fbiC 1302911 c.-20T>C upstream_gene_variant 0.13
fbiC 1303663 c.734_740delTGACCGA frameshift_variant 0.17
fbiC 1304168 c.1239_1254delTGTGGTGGCGCTGGCG frameshift_variant 0.17
fbiC 1304269 c.1340_1341delTC frameshift_variant 0.14
fbiC 1305268 p.Arg780Ser missense_variant 0.12
fbiC 1305288 c.2358C>T synonymous_variant 0.12
embR 1416918 p.Glu144Lys missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673602 p.Leu55Met missense_variant 0.33
rpsA 1833941 p.Val134Ile missense_variant 0.11
rpsA 1834544 p.Asp335Asn missense_variant 0.11
tlyA 1917785 c.-155C>A upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918376 p.Gly146Asp missense_variant 0.11
tlyA 1918590 c.651G>A synonymous_variant 0.11
ndh 2101682 p.Gly454Ala missense_variant 0.11
ndh 2102071 c.972C>G synonymous_variant 0.11
ndh 2102859 c.176_183delCCACCGGG frameshift_variant 0.25
katG 2154990 c.1122C>A synonymous_variant 0.22
katG 2156349 c.-238G>T upstream_gene_variant 0.2
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714373 c.960C>T synonymous_variant 0.13
eis 2714464 p.Arg290His missense_variant 0.18
eis 2715014 p.Arg107Cys missense_variant 0.33
eis 2715117 c.216T>A synonymous_variant 0.25
eis 2715395 c.-63C>T upstream_gene_variant 0.17
folC 2747736 c.-138G>A upstream_gene_variant 0.18
pepQ 2859965 p.Ala152Ser missense_variant 0.2
pepQ 2860555 c.-137A>G upstream_gene_variant 0.14
ribD 2986647 c.-192G>A upstream_gene_variant 0.15
ribD 2986871 c.33C>T synonymous_variant 0.17
ribD 2987092 p.Val85Ala missense_variant 0.2
ribD 2987140 p.Val101Ala missense_variant 0.11
thyX 3067474 p.Pro158Ala missense_variant 1.0
thyX 3067476 p.Gln157Leu missense_variant 0.17
Rv3083 3448567 p.His22Asp missense_variant 0.92
Rv3083 3448593 c.90G>A synonymous_variant 0.18
Rv3083 3448673 p.Ser57Phe missense_variant 0.2
Rv3083 3448732 p.Asp77Asn missense_variant 0.15
Rv3083 3449462 p.Gln320Leu missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568735 c.-56G>A upstream_gene_variant 0.18
Rv3236c 3612410 p.Leu236Pro missense_variant 0.14
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
fbiB 3641731 c.201delC frameshift_variant 0.15
fbiB 3642277 p.Ala248Val missense_variant 0.12
rpoA 3877510 p.Glu333Val missense_variant 0.11
rpoA 3878051 p.Arg153Trp missense_variant 0.13
rpoA 3878526 c.-19G>A upstream_gene_variant 0.29
rpoA 3878700 c.-193C>T upstream_gene_variant 0.25
clpC1 4038976 p.Leu577Ile missense_variant 0.2
clpC1 4039553 c.1152C>T synonymous_variant 0.13
clpC1 4040221 p.Ser162Pro missense_variant 0.13
clpC1 4040550 p.Leu52Ser missense_variant 0.11
clpC1 4040771 c.-68delT upstream_gene_variant 0.13
embC 4240006 c.144A>G synonymous_variant 1.0
embC 4241132 p.Pro424Thr missense_variant 0.18
embC 4241606 p.Thr582Ala missense_variant 0.22
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245287 p.Leu685Phe missense_variant 0.15
embB 4246648 c.135G>T synonymous_variant 0.1
embB 4247376 p.Leu288Pro missense_variant 0.12
embB 4248585 p.Arg691Pro missense_variant 0.12
embB 4249646 p.Arg1045Trp missense_variant 0.33
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4269396 c.-560G>A upstream_gene_variant 0.12
aftB 4269642 c.-806G>A upstream_gene_variant 0.15
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338377 p.Ala49Thr missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0