TB-Profiler result

Run: ERR11050214
Summary

Run ID: ERR11050214

Sample name:

Date: 02-04-2023 16:23:18

Number of reads: 624938

Percentage reads mapped: 99.63

Strain: lineage4.8

Drug-resistance: Sensitive

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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
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
gyrB 5505 p.His89Arg missense_variant 0.1
gyrB 5887 c.648C>T synonymous_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 0.95
gyrA 9649 p.Val783Gly missense_variant 0.4
fgd1 490756 c.-27T>G upstream_gene_variant 0.12
mshA 576609 p.Ala421Gly missense_variant 0.75
mshA 576613 c.1266A>C synonymous_variant 1.0
rpoB 759738 c.-69G>C upstream_gene_variant 0.25
rpoB 760004 c.198A>G synonymous_variant 0.11
rpoB 760933 p.Gly376Asp missense_variant 0.12
rpoC 765928 c.2559C>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776453 p.Met676Ile missense_variant 0.12
mmpL5 777231 p.Asp417Ala missense_variant 0.33
mmpL5 777391 p.Phe364Val missense_variant 0.27
mmpL5 777978 p.Ala168Val missense_variant 0.15
mmpR5 779086 p.Thr33Ala missense_variant 0.12
mmpR5 779104 p.Leu39Val missense_variant 0.15
mmpR5 779381 p.Gln131Leu missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305043 p.Ser705Pro missense_variant 0.1
Rv1258c 1407177 p.Leu55Arg missense_variant 0.22
Rv1258c 1407308 c.33G>A synonymous_variant 0.18
embR 1416430 c.918G>C synonymous_variant 0.18
embR 1417096 c.252T>G synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472762 n.917C>T non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.24
fabG1 1673553 p.Asp38Glu missense_variant 0.71
rpsA 1834914 p.Lys458Thr missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918382 p.Val148Gly missense_variant 0.25
tlyA 1918621 p.Ser228Arg missense_variant 0.22
ndh 2102817 p.Leu76Val missense_variant 0.33
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2222676 c.488delA frameshift_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288877 p.Gln122Arg missense_variant 0.2
pncA 2289786 c.-545G>C upstream_gene_variant 0.3
kasA 2519071 p.Asp319Glu missense_variant 0.18
eis 2715237 c.96A>G synonymous_variant 0.2
pepQ 2859507 p.Glu304Asp missense_variant 0.18
pepQ 2859933 c.486C>G synonymous_variant 0.27
Rv2752c 3064823 p.Val457Leu missense_variant 0.17
ald 3087649 p.Gly277Asp missense_variant 0.13
ald 3087816 p.Cys333Gly missense_variant 0.38
fprA 3473910 c.-97T>A upstream_gene_variant 0.15
fprA 3474289 p.Glu95Gln missense_variant 0.22
fbiB 3641756 c.222C>T synonymous_variant 0.15
alr 3841536 c.-116A>G upstream_gene_variant 0.12
rpoA 3877633 c.873_874delGA frameshift_variant 0.18
rpoA 3877769 p.Phe247Ile missense_variant 0.2
rpoA 3878354 p.Thr52Pro missense_variant 0.17
clpC1 4039612 c.1093C>A synonymous_variant 0.12
clpC1 4039729 p.Asp326Asn missense_variant 1.0
panD 4044255 p.Lys9Asn missense_variant 0.12
embC 4242331 p.Glu823Asp missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243585 p.Phe118Ser missense_variant 0.21
embA 4243682 c.450T>G synonymous_variant 0.3
embA 4244029 p.Val266Ala missense_variant 0.11
aftB 4267400 c.1437G>C synonymous_variant 0.33
aftB 4268892 c.-56T>G upstream_gene_variant 0.23
ethR 4327787 p.Val80Gly missense_variant 1.0
ethA 4328025 c.-552T>G upstream_gene_variant 0.29
ethA 4328415 c.-942A>G upstream_gene_variant 0.25
whiB6 4338200 p.Asp108His missense_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0