TB-Profiler result

Run: ERR6865753
Summary

Run ID: ERR6865753

Sample name:

Date: 02-04-2023 03:04:19

Number of reads: 1967481

Percentage reads mapped: 92.27

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.97 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289099 p.Lys48Thr missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326341 p.Pro378Leu missense_variant 1.0 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.13
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.13
rrs 1473115 n.1270G>C non_coding_transcript_exon_variant 0.12
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.13
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.14
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.1
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.1
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.12
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.12
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.11
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.11
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.1
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.12
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.11
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.11
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.11
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.11
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.21
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.21
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.16
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.16
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.15
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.16
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.16
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.17
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.17
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.17
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.17
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.17
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.16
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.16
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243392 p.Asn54Asp missense_variant 1.0
ubiA 4269731 p.Ala35Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407986 p.Gly73Arg missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0