TB-Profiler result

Run: ERR040138
Summary

Run ID: ERR040138

Sample name:

Date: 31-03-2023 08:48:11

Number of reads: 14569755

Percentage reads mapped: 99.34

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 None 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 761100 p.Gln432Lys missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.2
rpoB 762249 p.Leu815Val missense_variant 0.22
rpoC 762836 c.-534C>G upstream_gene_variant 0.45
rpoC 764725 p.Phe452Leu missense_variant 0.2
rpoC 766710 p.Gly1114Val missense_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.19
atpE 1461019 c.-26C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.3
inhA 1674952 p.Pro251Ala missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.23
PPE35 2169866 c.747G>C synonymous_variant 0.28
eis 2714366 p.Val323Leu missense_variant 0.22
eis 2715072 c.261G>A synonymous_variant 1.0
folC 2746186 c.1413G>C synonymous_variant 0.2
pepQ 2859381 c.1038C>G synonymous_variant 0.21
ribD 2987307 p.Ala157Pro missense_variant 0.17
thyA 3073806 c.666C>G synonymous_variant 0.19
thyA 3073817 p.Gln219Glu missense_variant 0.26
Rv3083 3448388 c.-116C>T upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.23
clpC1 4038857 c.1848C>A synonymous_variant 0.16
clpC1 4039932 p.Gly258Val missense_variant 0.27
panD 4043967 c.315C>T synonymous_variant 1.0
embC 4239842 c.-21C>A upstream_gene_variant 0.18
embC 4242425 p.Arg855Gly missense_variant 0.16
embC 4242476 p.Pro872Ala missense_variant 0.23
embC 4242822 p.Val987Gly missense_variant 0.38
embC 4242827 p.Leu989Val missense_variant 0.19
ubiA 4269529 p.Ala102Gly missense_variant 0.23
ethA 4327672 c.-199G>A upstream_gene_variant 0.28
ethR 4328122 p.Pro192Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0