TB-Profiler result

Run: ERR2652991
Summary

Run ID: ERR2652991

Sample name:

Date: 31-03-2023 22:26:04

Number of reads: 962662

Percentage reads mapped: 86.87

Strain: lineage4.3.4.2.1

Drug-resistance: Pre-XDR-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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.98
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.98
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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155699 p.Asn138Ser missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 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 6140 p.Val301Leu 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
rpoB 760336 p.Pro177Leu missense_variant 0.12
rpoC 764490 p.Leu374Pro missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765461 p.Asn698His missense_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 1472936 n.1091C>T non_coding_transcript_exon_variant 0.19
rrs 1472953 n.1109dupT non_coding_transcript_exon_variant 0.13
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.21
rrs 1472958 n.1114delT non_coding_transcript_exon_variant 0.14
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.21
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.21
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.21
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.21
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.2
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.2
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.19
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.18
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.17
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.17
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.17
rrl 1476023 n.2366C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.1
fabG1 1673771 p.Ala111Asp missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169399 p.Gly405Asp missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065365 p.Leu276Pro missense_variant 0.91
thyA 3073868 p.Thr202Ala missense_variant 0.97
thyA 3074167 p.Pro102Arg missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3878076 c.432C>T synonymous_variant 0.94
rpoA 3878630 c.-123G>C upstream_gene_variant 0.19
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326900 p.Pro192Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0