TB-Profiler result

Run: ERR2229165
Summary

Run ID: ERR2229165

Sample name:

Date: 31-03-2023 16:46:16

Number of reads: 227354

Percentage reads mapped: 98.89

Strain: lineage4

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
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
mshA 575904 p.Ala186Glu missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 1.0
rpoB 762071 p.Asp755Glu missense_variant 0.5
rpoB 763083 p.Arg1093Ser missense_variant 0.4
rpoB 763305 p.Ser1167Cys missense_variant 0.18
mmpL5 776958 p.Gln508Leu missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416265 c.1083C>A synonymous_variant 0.13
embR 1416622 c.726C>T synonymous_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1833681 p.Asp47Gly missense_variant 0.33
rpsA 1834322 p.Glu261* stop_gained 0.33
ndh 2102796 p.Gln83* stop_gained 0.5
PPE35 2167745 p.Thr956Arg missense_variant 0.17
PPE35 2167814 c.2799C>T synonymous_variant 0.17
PPE35 2167965 p.Ala883Gly missense_variant 0.45
PPE35 2167967 c.2646A>C synonymous_variant 0.45
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169272 c.1341C>G synonymous_variant 0.2
PPE35 2169278 c.1335T>C synonymous_variant 0.2
PPE35 2169281 c.1332T>G synonymous_variant 0.2
PPE35 2169287 c.1326T>C synonymous_variant 0.2
PPE35 2169902 p.Leu237Phe missense_variant 0.23
PPE35 2169910 p.Asn235Tyr missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.41
PPE35 2170053 p.Thr187Ser missense_variant 0.5
PPE35 2170779 c.-167A>G upstream_gene_variant 0.12
Rv1979c 2221969 p.Ser399Phe missense_variant 0.2
Rv1979c 2222416 p.Arg250Leu missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714327 p.Gly336Ser missense_variant 0.33
Rv2752c 3065143 p.Gly350Val missense_variant 0.25
ald 3087348 p.Gly177Ser missense_variant 0.4
ald 3087894 c.1076delT frameshift_variant 0.67
alr 3841546 c.-126C>A upstream_gene_variant 0.23
ddn 3987173 c.330C>A synonymous_variant 0.2
clpC1 4038653 c.2052C>T synonymous_variant 0.25
clpC1 4038679 p.Pro676Thr missense_variant 0.33
clpC1 4039645 p.His354Asp missense_variant 0.75
clpC1 4039654 p.Thr351Ser missense_variant 0.67
embA 4243755 p.Thr175Ala missense_variant 0.5
embA 4244184 p.Ser318Leu missense_variant 0.5
embA 4244324 c.1092T>C synonymous_variant 0.33
embA 4245364 p.Phe711Cys missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4246563 p.Leu17Trp missense_variant 0.4
embB 4246795 c.282G>A synonymous_variant 1.0
aftB 4267383 p.Ala485Gly missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0