TB-Profiler result

Run: SRR14807491
Summary

Run ID: SRR14807491

Sample name:

Date: 03-04-2023 12:24:58

Number of reads: 4115414

Percentage reads mapped: 99.65

Strain: lineage4.8;lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 0.29
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.69
lineage4.1.2 Euro-American T;H None 0.32
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.28
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
rpsL 781822 p.Lys88Arg missense_variant 0.23 streptomycin
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
gyrA 7585 p.Ser95Thr missense_variant 0.31
gyrA 9304 p.Gly668Asp missense_variant 0.28
fgd1 491424 c.650_655delCCGCTG disruptive_inframe_deletion 0.66
fgd1 491591 p.Lys270Met missense_variant 0.31
mshA 575679 p.Asn111Ser missense_variant 0.28
mshA 575915 p.Asp190Asn missense_variant 0.65
mshA 576108 p.Ala254Gly missense_variant 0.3
rpoB 760115 c.309C>T synonymous_variant 0.35
rpoC 765150 p.Gly594Glu missense_variant 0.37
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 0.74
rpsA 1834675 c.1134C>T synonymous_variant 0.34
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156219 c.-108A>T upstream_gene_variant 0.28
PPE35 2168149 p.Pro822Ser missense_variant 0.73
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.28
ald 3086788 c.-32T>C upstream_gene_variant 0.29
fbiD 3339734 p.Ala206Gly missense_variant 0.31
Rv3083 3448322 c.-182G>A upstream_gene_variant 0.71
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.26
rpoA 3878637 c.-130G>C upstream_gene_variant 0.26
embC 4240373 c.511C>T synonymous_variant 0.74
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.29
embA 4244849 c.1617C>T synonymous_variant 0.24
embB 4246584 p.Arg24Pro missense_variant 0.12
embB 4246904 p.Val131Met missense_variant 0.71
aftB 4269192 c.-356C>T upstream_gene_variant 0.69
whiB6 4338595 c.-75delG upstream_gene_variant 1.0