TB-Profiler result

Run: SRR18715286
Summary

Run ID: SRR18715286

Sample name:

Date: 03-04-2023 20:27:23

Number of reads: 4343003

Percentage reads mapped: 99.73

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 0.93
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.91
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 0.13 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 0.21
mshA 576113 p.Arg256Gly missense_variant 0.26
mshA 576456 p.Val370Gly missense_variant 0.27
mshA 576613 c.1266A>C synonymous_variant 0.29
mshA 576616 c.1269G>C synonymous_variant 0.35
ccsA 619794 c.-97C>T upstream_gene_variant 0.53
ccsA 620625 p.Ile245Met missense_variant 0.11
rpoC 764367 p.Gly333Ala missense_variant 0.3
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 0.89
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.94
fabG1 1673553 p.Asp38Glu missense_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.33
pepQ 2860159 p.Ala87Gly missense_variant 0.16
ald 3086779 c.-41C>A upstream_gene_variant 0.92
fbiD 3339734 p.Ala206Gly missense_variant 0.69
fbiD 3339746 p.Ala210Gly missense_variant 0.6
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.22
Rv3083 3448500 c.-4A>G upstream_gene_variant 0.19
Rv3083 3448501 c.-3G>T upstream_gene_variant 0.19
Rv3083 3449644 c.1146delC frameshift_variant 0.25
rpoA 3878597 c.-90G>C upstream_gene_variant 0.29
rpoA 3878613 c.-106A>C upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.68
embC 4240409 p.Pro183Ala missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.27
ubiA 4269059 p.Ile259Val missense_variant 0.93
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0