TB-Profiler result

Run: ERR2229496
Summary

Run ID: ERR2229496

Sample name:

Date: 31-03-2023 17:15:27

Number of reads: 366995

Percentage reads mapped: 99.26

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.33
rpoC 765031 p.Glu554Asp missense_variant 0.4
mmpL5 777482 c.999G>A synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801277 p.Pro157Thr missense_variant 0.33
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305264 c.2334C>T synonymous_variant 0.22
Rv1258c 1406797 p.Gly182Arg missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.14
rrs 1472124 n.279C>A non_coding_transcript_exon_variant 0.14
rrs 1472312 n.467G>T non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474328 n.675_677dupGAA non_coding_transcript_exon_variant 0.67
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.57
rpsA 1833440 c.-102G>T upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102074 p.Met323Lys missense_variant 0.3
ndh 2103225 c.-183A>C upstream_gene_variant 0.5
katG 2155318 p.Leu265Pro missense_variant 0.22
PPE35 2167965 p.Ala883Gly missense_variant 0.25
PPE35 2167967 c.2646A>C synonymous_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169386 c.1227C>A synonymous_variant 0.14
PPE35 2169394 p.Ala407Ser missense_variant 0.14
PPE35 2169397 p.Gly406Ser missense_variant 0.14
PPE35 2169866 c.747G>A synonymous_variant 0.13
PPE35 2169879 p.Phe245Ser missense_variant 0.26
PPE35 2169882 p.Ser244Asn missense_variant 0.27
PPE35 2169890 c.723C>T synonymous_variant 0.2
PPE35 2169893 c.720C>A synonymous_variant 0.21
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.55
PPE35 2170157 p.Ala152Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
whiB7 3568501 p.Ala60Asp missense_variant 0.25
ddn 3987144 p.Gln101* stop_gained 0.2
embC 4240757 p.Thr299Gly missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.4
embB 4248569 c.2056C>T synonymous_variant 0.15
ethR 4326961 c.-588G>C upstream_gene_variant 0.4
ethR 4326964 c.-585G>A upstream_gene_variant 0.4
ethR 4326970 c.-579G>T upstream_gene_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0