TB-Profiler result

Run: SRR21595941
Summary

Run ID: SRR21595941

Sample name:

Date: 04-04-2023 02:17:18

Number of reads: 706641

Percentage reads mapped: 99.35

Strain: lineage4.8

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
lineage4.8 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
gid 4408100 c.102delG frameshift_variant 1.0 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
mshA 576108 p.Ala254Gly missense_variant 0.24
mshA 576482 p.Val379Leu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778907 c.-427C>A upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416187 c.1160delG frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.4
fabG1 1673558 p.His40Pro missense_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288839 p.Thr135Ala missense_variant 1.0
ahpC 2726436 p.Ile82Val missense_variant 0.12
ahpC 2726701 p.Ser170Phe missense_variant 0.12
pepQ 2860259 p.Leu54Val missense_variant 1.0
pepQ 2860402 p.Arg6His missense_variant 0.12
ribD 2986890 p.Ser18Gly missense_variant 0.1
fbiD 3339734 p.Ala206Gly missense_variant 0.22
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
whiB7 3568428 c.252A>C synonymous_variant 0.23
alr 3840764 c.657G>C synonymous_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.33
clpC1 4038666 p.Gly680Asp missense_variant 0.12
clpC1 4039337 c.1368A>C synonymous_variant 1.0
clpC1 4040421 p.Ala95Val missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242659 c.-574C>T upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.15
aftB 4267623 p.Ser405Trp missense_variant 0.11
ethA 4326358 p.Met372Ile missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0