TB-Profiler result

Run: SRR6484999

Summary

Run ID: SRR6484999

Sample name:

Date: 04-04-2023 15:01:37

Number of reads: 7241019

Percentage reads mapped: 99.67

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 0.98
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.92
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 0.12 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
fgd1 491742 c.960T>C synonymous_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.11
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 0.92
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.14
PPE35 2168076 p.Thr846Met missense_variant 0.93
PPE35 2168149 p.Pro822Ser missense_variant 0.93
PPE35 2170048 p.Leu189Val missense_variant 0.19
PPE35 2170053 p.Thr187Ser missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.75
Rv3083 3449609 p.Glu369Val missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.12
embB 4246584 p.Arg24Pro missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv1979c 2222416 c.-597_748del frameshift_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0