TB-Profiler result

Run: SRR23862131
Summary

Run ID: SRR23862131

Sample name:

Date: 12-04-2023 20:00:18

Number of reads: 4576693

Percentage reads mapped: 99.84

Strain: lineage4.8

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
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 576100 p.Asp251Glu missense_variant 0.19
mshA 576456 p.Val370Gly missense_variant 0.24
mshA 576468 p.Val374Gly missense_variant 0.21
mshA 576626 p.Thr427Pro missense_variant 0.28
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801452 p.Gly215Asp missense_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
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fbiD 3339726 c.609A>C synonymous_variant 0.15
fbiD 3339740 p.Ala208Gly missense_variant 0.25
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.18
whiB7 3568428 c.252A>G synonymous_variant 0.24
whiB7 3568431 c.249C>G synonymous_variant 0.15
whiB7 3568437 c.243T>C synonymous_variant 0.17
rpoA 3878589 c.-82A>T upstream_gene_variant 0.23
rpoA 3878597 c.-90G>C upstream_gene_variant 0.2
rpoA 3878598 c.-91C>G upstream_gene_variant 0.2
rpoA 3878601 c.-94C>G upstream_gene_variant 0.18
rpoA 3878608 c.-101C>G upstream_gene_variant 0.46
rpoA 3878609 c.-102T>G upstream_gene_variant 0.27
rpoA 3878613 c.-106A>C upstream_gene_variant 0.31
rpoA 3878618 c.-111A>C upstream_gene_variant 0.36
rpoA 3878641 c.-134C>G upstream_gene_variant 0.18
rpoA 3878658 c.-151A>C upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246974 p.His154Pro missense_variant 0.17
embB 4247007 p.Lys165Thr missense_variant 0.22
embB 4247010 p.Asp166Ala missense_variant 0.16
embB 4247015 p.Ser168Ala missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0