TB-Profiler result

Run: SRR9940972
Summary

Run ID: SRR9940972

Sample name:

Date: 04-04-2023 23:02:02

Number of reads: 457548

Percentage reads mapped: 99.62

Strain: lineage4.9

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
lineage4.9 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
ethA 4327172 c.301delC frameshift_variant 0.13 ethionamide
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
ccsA 620375 p.Pro162Leu missense_variant 0.11
rpoB 760469 p.Asp221Glu missense_variant 0.13
rpoB 761501 c.1698delC frameshift_variant 0.11
rpoC 765248 c.1879T>C synonymous_variant 0.14
mmpL5 776161 p.Tyr774His missense_variant 0.18
mmpL5 776574 p.Ala636Val missense_variant 0.12
mmpL5 776934 p.Gln516Arg missense_variant 0.12
mmpR5 779454 c.466dupC frameshift_variant 0.82
fbiC 1303016 p.Val29Gly missense_variant 0.29
fbiC 1305245 p.Leu772Ser missense_variant 0.14
Rv1258c 1406677 c.664C>T synonymous_variant 0.18
atpE 1461272 c.228C>T synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475490 n.1833C>A non_coding_transcript_exon_variant 0.12
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.18
rpsA 1834893 p.Ala451Gly missense_variant 0.2
katG 2155072 p.Pro347His missense_variant 0.17
katG 2155767 c.345C>A synonymous_variant 0.2
PPE35 2170191 p.Glu141Ala missense_variant 0.29
PPE35 2170598 c.15G>A synonymous_variant 1.0
PPE35 2170756 c.-144G>A upstream_gene_variant 0.2
pepQ 2860108 p.Val104Ala missense_variant 0.22
pepQ 2860339 p.Leu27Pro missense_variant 0.18
pepQ 2860540 c.-122T>C upstream_gene_variant 0.11
pepQ 2860617 c.-199C>G upstream_gene_variant 0.15
thyA 3073912 c.558_559delCA frameshift_variant 0.11
thyA 3074246 p.Gly76Arg missense_variant 0.12
ald 3087107 c.288T>C synonymous_variant 0.29
ald 3087236 c.417A>T synonymous_variant 0.18
whiB7 3568642 p.Gln13Arg missense_variant 0.1
whiB7 3568877 c.-198C>A upstream_gene_variant 0.14
Rv3236c 3612006 p.Arg371Ser missense_variant 0.33
Rv3236c 3612222 c.894dupC frameshift_variant 0.13
fbiA 3640357 c.-186G>A upstream_gene_variant 0.2
clpC1 4038711 p.Thr665Arg missense_variant 0.17
clpC1 4040089 c.616C>A synonymous_variant 0.1
panD 4044339 c.-58C>A upstream_gene_variant 0.22
embC 4239682 c.-181T>C upstream_gene_variant 0.17
embC 4240885 c.1023T>C synonymous_variant 0.12
embC 4241368 c.1506C>A synonymous_variant 0.17
embC 4241540 p.Thr560Pro missense_variant 0.25
embC 4242596 p.Gly912Cys missense_variant 0.29
embA 4242856 c.-377C>T upstream_gene_variant 0.12
embB 4246534 p.Arg7Ser missense_variant 0.22
embB 4248438 p.Thr642Ser missense_variant 0.12
aftB 4268540 p.Met99Ile missense_variant 0.5