TB-Profiler result

Run: ERR2124081
Summary

Run ID: ERR2124081

Sample name:

Date: 31-03-2023 15:51:09

Number of reads: 6279755

Percentage reads mapped: 99.38

Strain: lineage4.6.1.2

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 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.99
lineage4.6.1.2 Euro-American T2 RD724 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 0.99 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289114 p.His43Pro missense_variant 0.98 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.96 ethambutol
ethA 4326249 c.1215_1224delGTTGAATTAC frameshift_variant 1.0 ethionamide, 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764660 p.Val431Met missense_variant 0.98
rpoC 764810 p.Pro481Thr missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.12
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.12
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.14
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.16
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.23
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.26
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.29
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.26
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.28
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.3
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.24
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.25
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.32
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.32
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.25
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.26
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.18
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.19
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.19
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.19
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.2
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.29
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.13
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.17
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.21
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.18
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.14
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.14
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.18
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.2
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.19
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.32
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.27
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.37
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.3
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.46
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.15
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.25
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.21
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.24
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.23
rrl 1475289 n.1632G>A non_coding_transcript_exon_variant 0.23
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.23
rrl 1475297 n.1640C>T non_coding_transcript_exon_variant 0.29
rrl 1475315 n.1658A>C non_coding_transcript_exon_variant 0.19
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.12
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.18
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.14
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.14
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.18
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.12
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.12
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.17
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.25
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.11
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.1
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.13
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170692 c.-80T>G upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714308 p.Pro342Leu missense_variant 1.0
Rv2752c 3065920 p.Pro91Leu missense_variant 0.98
thyA 3073806 c.666C>G synonymous_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
embC 4242425 p.Arg855Gly missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 1.0
ubiA 4269124 p.Ala237Val missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408094 p.Gly37Arg missense_variant 0.97