TB-Profiler result

Run: SRR16088244
Summary

Run ID: SRR16088244

Sample name:

Date: 03-04-2023 16:05:13

Number of reads: 4677038

Percentage reads mapped: 99.7

Strain: lineage4.8

Drug-resistance: Other

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
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 9647 c.2346C>G synonymous_variant 0.2
mshA 576613 c.1266A>C synonymous_variant 0.29
mshA 576616 c.1269G>C synonymous_variant 0.31
rpoC 764367 p.Gly333Ala missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.24
pepQ 2860159 p.Ala87Gly missense_variant 0.16
fbiD 3339734 p.Ala206Gly missense_variant 0.56
fbiD 3339744 c.627A>T synonymous_variant 0.33
fbiD 3339746 p.Ala210Gly missense_variant 0.2
Rv3083 3448322 c.-182G>A upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.31
rpoA 3878597 c.-90G>C upstream_gene_variant 0.46
rpoA 3878630 c.-123G>C upstream_gene_variant 0.5
rpoA 3878637 c.-130G>C upstream_gene_variant 0.29
rpoA 3878641 c.-134C>G upstream_gene_variant 0.7
embC 4240409 p.Pro183Ala missense_variant 0.42
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.23
embB 4246584 p.Arg24Pro missense_variant 0.16
embB 4247016 p.Ser168Trp missense_variant 0.23
embB 4247020 c.507C>G synonymous_variant 0.24
embB 4248328 c.1815G>C synonymous_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0