TB-Profiler result

Run: ERR2229411
Summary

Run ID: ERR2229411

Sample name:

Date: 31-03-2023 17:10:05

Number of reads: 376512

Percentage reads mapped: 99.2

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 7347 p.Glu16Lys missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8089 p.Ser263Tyr missense_variant 0.29
gyrA 8864 c.1563C>A synonymous_variant 0.15
mshA 575527 c.180G>T synonymous_variant 0.15
mshA 576674 p.Arg443Ser missense_variant 0.29
ccsA 620539 p.Arg217Gly missense_variant 0.4
rpoC 764237 p.Leu290Ile missense_variant 0.17
rpoC 764601 p.Gly411Ala missense_variant 0.2
rpoC 765124 c.1755G>T synonymous_variant 0.18
rpoC 765217 c.1848C>T synonymous_variant 0.2
rpoC 766406 p.Arg1013Ser missense_variant 0.22
rpoC 767276 p.Ala1303Ser missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781765 p.Gly69Val missense_variant 0.15
rplC 800689 c.-120G>A upstream_gene_variant 0.17
fbiC 1303051 p.Val41Met missense_variant 0.17
fbiC 1303168 p.Gly80Cys missense_variant 0.12
fbiC 1303213 p.Thr95Ala missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407005 p.Leu112Arg missense_variant 0.2
Rv1258c 1407059 p.Trp94Cys missense_variant 0.25
embR 1416808 c.540C>A synonymous_variant 0.12
embR 1417063 c.285C>T synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471953 n.108G>T non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474908 n.1251G>T non_coding_transcript_exon_variant 0.29
fabG1 1673374 c.-66C>A upstream_gene_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918367 p.Ala143Val missense_variant 0.14
ndh 2103135 c.-93A>G upstream_gene_variant 0.4
PPE35 2168485 p.Asn710Tyr missense_variant 0.25
PPE35 2168517 c.2095delA frameshift_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.14
PPE35 2169272 c.1341C>G synonymous_variant 0.15
PPE35 2169695 c.918A>G synonymous_variant 0.12
PPE35 2169703 p.Asn304Asp missense_variant 0.11
PPE35 2169704 c.909A>C synonymous_variant 0.11
PPE35 2169707 p.Thr302Ser missense_variant 0.12
PPE35 2169717 p.Asn299Ile missense_variant 0.18
PPE35 2169875 c.738T>C synonymous_variant 0.11
PPE35 2169884 c.729T>C synonymous_variant 0.11
PPE35 2169902 c.711G>C synonymous_variant 0.11
PPE35 2169910 p.Asn235Tyr missense_variant 0.12
PPE35 2170169 c.444A>G synonymous_variant 0.12
Rv1979c 2223049 p.Val39Ala missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714464 p.Arg290His missense_variant 0.22
ahpC 2726276 c.84C>A synonymous_variant 0.17
folC 2746965 p.Ile212Phe missense_variant 0.22
ribD 2987350 p.Gly171Ala missense_variant 0.4
Rv2752c 3067063 c.-872C>T upstream_gene_variant 0.18
thyX 3067410 p.Thr179Ile missense_variant 0.17
thyA 3074565 c.-94C>T upstream_gene_variant 0.33
thyA 3074580 c.-109T>C upstream_gene_variant 0.33
thyA 3074637 c.-166A>G upstream_gene_variant 0.5
fbiD 3339350 p.Asp78Gly missense_variant 0.15
fbiD 3339354 c.237A>G synonymous_variant 0.15
fbiD 3339510 c.393C>A synonymous_variant 0.22
Rv3083 3448346 c.-158C>A upstream_gene_variant 0.14
fprA 3474254 p.Val83Asp missense_variant 0.17
fprA 3474766 p.Gly254Ser missense_variant 0.18
fbiB 3641205 c.-330C>A upstream_gene_variant 0.2
fbiA 3641411 p.Val290Ala missense_variant 0.15
fbiB 3642876 p.Lys448Glu missense_variant 0.29
alr 3840491 c.930G>T synonymous_variant 0.2
alr 3841582 c.-162A>G upstream_gene_variant 0.12
alr 3841589 c.-170delG upstream_gene_variant 0.12
clpC1 4039526 c.1179G>C synonymous_variant 0.3
clpC1 4039530 p.Asp392Ala missense_variant 0.33
clpC1 4039691 c.1014G>C synonymous_variant 0.11
clpC1 4039714 p.Tyr331His missense_variant 0.17
clpC1 4039730 c.975C>G synonymous_variant 0.2
clpC1 4040878 c.-174T>G upstream_gene_variant 0.21
embC 4240987 c.1125G>T synonymous_variant 0.5
embC 4241254 c.1392C>T synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243516 p.Ala95Asp missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407627 c.576C>T synonymous_variant 0.17
gid 4407775 p.Asp143Val missense_variant 0.14
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0