TB-Profiler result

Run: SRR18715278
Summary

Run ID: SRR18715278

Sample name:

Date: 03-04-2023 20:26:55

Number of reads: 2460312

Percentage reads mapped: 99.68

Strain: lineage4.8

Drug-resistance: HR-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
lineage4.8 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
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
mshA 576456 p.Val370Gly missense_variant 0.27
mshA 576606 p.Ala420Gly missense_variant 0.26
mshA 576616 c.1269G>C synonymous_variant 0.25
rpoC 764367 p.Gly333Ala missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.31
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
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.31
fabG1 1673553 p.Asp38Glu missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2222734 p.Phe144Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.22
pepQ 2860159 p.Ala87Gly missense_variant 0.2
ald 3087816 p.Cys333Gly missense_variant 0.12
fbiD 3339751 p.Ala212Pro missense_variant 0.33
Rv3083 3448360 c.-144C>G upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568431 c.249C>G synonymous_variant 0.3
rpoA 3878641 c.-134C>G upstream_gene_variant 0.55
embC 4240409 p.Pro183Ala missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.28
embB 4247016 p.Ser168Trp missense_variant 0.25
embB 4248328 c.1815G>C synonymous_variant 0.35
aftB 4267400 c.1437G>C synonymous_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407758 p.Ser149Arg missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0