TB-Profiler result

Run: ERR2229107
Summary

Run ID: ERR2229107

Sample name:

Date: 31-03-2023 16:39:47

Number of reads: 535043

Percentage reads mapped: 99.39

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
gyrA 9608 p.Asp769Glu missense_variant 0.18
mshA 575932 c.585G>A synonymous_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.5
rpoB 761390 p.Asp528Glu missense_variant 0.18
rpoB 762344 c.2542delT frameshift_variant 0.12
rpoB 763096 p.Tyr1097Phe missense_variant 0.29
rpoC 763659 p.Leu97His missense_variant 0.12
rpoC 763669 c.300C>T synonymous_variant 0.12
rpoC 766773 p.Val1135Asp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777898 p.Asp195Tyr missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781833 c.278_279dupTG frameshift_variant 0.18
rpsL 781888 p.Arg110His missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471788 n.-58G>C upstream_gene_variant 0.12
rrs 1473000 n.1155G>T non_coding_transcript_exon_variant 1.0
rrl 1475406 n.1749T>C non_coding_transcript_exon_variant 0.12
rrl 1475486 n.1829A>G non_coding_transcript_exon_variant 0.17
rrl 1476562 n.2905C>A non_coding_transcript_exon_variant 0.33
fabG1 1673346 c.-94C>G upstream_gene_variant 0.17
fabG1 1673349 c.-91G>C upstream_gene_variant 0.17
fabG1 1673357 c.-83G>A upstream_gene_variant 0.25
fabG1 1673359 c.-81T>C upstream_gene_variant 0.25
fabG1 1673361 c.-79C>G upstream_gene_variant 0.25
fabG1 1673380 c.-60C>G upstream_gene_variant 0.57
inhA 1673943 c.-259C>A upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102175 p.Ala290Ser missense_variant 0.14
ndh 2102939 p.Arg35Leu missense_variant 0.13
PPE35 2167865 c.2748G>C synonymous_variant 0.22
PPE35 2167868 c.2745A>C synonymous_variant 0.22
PPE35 2167878 p.Ser912Asn missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.2
PPE35 2169272 c.1341C>G synonymous_variant 0.22
PPE35 2169278 c.1335T>C synonymous_variant 0.2
PPE35 2169281 c.1332T>G synonymous_variant 0.21
PPE35 2170048 p.Leu189Val missense_variant 0.39
PPE35 2170053 p.Thr187Ser missense_variant 0.41
PPE35 2170147 p.Ser156Ala missense_variant 0.14
PPE35 2170159 p.Ala152Ser missense_variant 0.13
PPE35 2170518 p.Asp32Thr missense_variant 0.12
PPE35 2170540 c.73C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223353 c.-189T>A upstream_gene_variant 0.12
pncA 2290069 c.-828C>A upstream_gene_variant 0.22
kasA 2518606 c.492G>C synonymous_variant 0.22
kasA 2518609 p.Met165Ile missense_variant 0.24
eis 2714224 p.Ala370Asp missense_variant 0.14
eis 2714753 p.Gln194Lys missense_variant 0.15
ahpC 2726461 p.Glu90Val missense_variant 0.17
thyA 3073925 p.Leu183Met missense_variant 0.2
thyA 3074210 p.Gly88Ser missense_variant 0.15
ald 3087035 c.216C>G synonymous_variant 0.11
fprA 3474142 c.141delG frameshift_variant 0.22
Rv3236c 3613060 c.57G>T synonymous_variant 0.22
fbiA 3640354 c.-189C>T upstream_gene_variant 0.15
fbiA 3640988 p.Arg149His missense_variant 0.13
fbiB 3641142 c.-393C>A upstream_gene_variant 0.29
fbiA 3641458 p.Val306Met missense_variant 0.22
fbiB 3641798 c.264C>A synonymous_variant 0.18
clpC1 4039498 p.Ile403Val missense_variant 0.14
clpC1 4039508 c.1197G>C synonymous_variant 0.15
clpC1 4039524 c.1180_1181insATATCACCGCCCGCT conservative_inframe_insertion 0.15
clpC1 4039730 c.975C>G synonymous_variant 0.13
clpC1 4040057 c.648C>T synonymous_variant 0.18
embC 4239968 p.Ala36Pro missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245493 p.Pro754Gln missense_variant 0.17
embB 4249620 p.Leu1036Gln missense_variant 0.25
aftB 4267775 c.1062T>C synonymous_variant 0.17
ethA 4326388 p.Asp362Glu missense_variant 0.22
ethR 4327673 c.127delG frameshift_variant 0.17
ethA 4328070 c.-597C>A upstream_gene_variant 0.18
ethR 4328138 p.Ala197Val missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0