TB-Profiler result

Run: SRR6930935
Summary

Run ID: SRR6930935

Sample name:

Date: 04-04-2023 18:13:55

Number of reads: 3610141

Percentage reads mapped: 99.65

Strain: lineage4.8

Drug-resistance: Pre-XDR-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
gyrB 6736 p.Asn499Lys missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2156110 p.Val1Ala missense_variant 1.0 isoniazid
pncA 2288817 p.Thr142Met missense_variant 0.99 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.98 ethambutol
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
rpoB 759939 p.Pro45Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
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 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154890 p.Phe408Leu missense_variant 1.0
katG 2156531 c.-435_-421delTGCGCGTGACCCGAC upstream_gene_variant 1.0
PPE35 2168446 p.Pro723Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288839 p.Thr135Ala missense_variant 0.99
ahpC 2726110 c.-83_-82insTC upstream_gene_variant 1.0
Rv2752c 3065855 c.336delT frameshift_variant 0.99
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.75
alr 3840764 c.657G>C synonymous_variant 0.99
clpC1 4039337 c.1368A>C synonymous_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338648 c.-127A>G upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0