TB-Profiler result

Run: ERR1213889
Summary

Run ID: ERR1213889

Sample name:

Date: 31-03-2023 12:42:43

Number of reads: 5503582

Percentage reads mapped: 98.73

Strain: lineage4.3.4.2.1

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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.99
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 0.98 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288731 p.Ala171Pro missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247402 p.Ser297Ala 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
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 1472035 n.190G>T non_coding_transcript_exon_variant 0.14
rrs 1472042 n.197T>C non_coding_transcript_exon_variant 0.15
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.19
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.25
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.24
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.2
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.22
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.25
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.26
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.33
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.25
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.25
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.38
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.14
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.14
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.13
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.12
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.18
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.15
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.17
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.12
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.18
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.16
rrl 1475028 n.1371G>A non_coding_transcript_exon_variant 0.13
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.13
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.12
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.12
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.12
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.16
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.14
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.16
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.16
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860017 c.402T>C synonymous_variant 1.0
Rv2752c 3065695 p.Leu166Pro missense_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.23
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
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3877967 p.Thr181Ser missense_variant 1.0
rpoA 3878641 c.-135delG upstream_gene_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.2
embC 4239686 c.-177C>A upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408125 p.Leu26Phe missense_variant 0.98
gid 4408156 p.Leu16Arg missense_variant 1.0