TB-Profiler result

Run: SRR14782413
Summary

Run ID: SRR14782413

Sample name:

Date: 03-04-2023 11:24:47

Number of reads: 2693262

Percentage reads mapped: 99.61

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 0.99
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
ddn 3987107 p.Trp88* stop_gained 1.0 delamanid
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 7496 c.195C>G synonymous_variant 0.99
gyrA 9647 c.2346C>G synonymous_variant 0.18
mshA 576108 p.Ala254Gly missense_variant 0.16
mshA 576483 p.Val379Gly missense_variant 0.25
mshA 576616 c.1269G>C synonymous_variant 0.27
rpoB 760742 c.936G>A synonymous_variant 0.98
rpoC 764367 p.Gly333Ala missense_variant 0.18
rpoC 764534 p.Arg389Gly missense_variant 0.14
rpoC 765369 p.Thr667Met missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.15
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 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518807 c.693C>T synonymous_variant 0.98
kasA 2519071 p.Asp319Glu missense_variant 0.16
pepQ 2860159 p.Ala87Gly missense_variant 0.23
Rv2752c 3064823 p.Val457Leu missense_variant 0.17
fbiD 3339734 p.Ala206Gly missense_variant 0.82
whiB7 3568428 c.252A>G synonymous_variant 0.5
whiB7 3568431 c.249C>G synonymous_variant 0.16
rpoA 3878597 c.-90G>C upstream_gene_variant 0.33
rpoA 3878637 c.-130G>C upstream_gene_variant 0.43
rpoA 3878641 c.-134C>G upstream_gene_variant 0.53
embC 4240409 p.Pro183Ala missense_variant 0.44
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.26
embB 4246529 p.Ser6Arg missense_variant 0.64
embB 4248324 p.Ala604Gly missense_variant 0.18
embB 4248328 c.1815G>C synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0