TB-Profiler result

Run: ERR5866550
Summary

Run ID: ERR5866550

Sample name:

Date: 02-04-2023 00:45:37

Number of reads: 1045103

Percentage reads mapped: 99.73

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 761139 p.His445Asp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 5559 p.Gly107Asp missense_variant 0.17
gyrB 6290 c.1051C>A synonymous_variant 0.19
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
fbiC 1303095 c.165G>A synonymous_variant 1.0
fbiC 1304768 p.Gly613Val missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473690 n.33T>C non_coding_transcript_exon_variant 0.13
rrl 1474286 n.629C>A non_coding_transcript_exon_variant 0.17
rrl 1475136 n.1479G>T non_coding_transcript_exon_variant 0.25
rrl 1476117 n.2460G>T non_coding_transcript_exon_variant 0.22
rrl 1476129 n.2472G>A non_coding_transcript_exon_variant 0.22
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2170534 p.Ala27Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746340 p.Ala420Val 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
clpC1 4038968 c.1737G>A synonymous_variant 0.86
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247215 c.702C>A synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407805 p.Ala133Gly missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0