TB-Profiler result

Run: ERR1577245
Summary

Run ID: ERR1577245

Sample name:

Date: 31-03-2023 14:38:52

Number of reads: 1006404

Percentage reads mapped: 98.4

Strain: lineage2.2.1

Drug-resistance: HR-TB

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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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2154581 c.1530delC frameshift_variant 0.17 isoniazid
embB 4247850 p.Pro446His missense_variant 0.18 ethambutol
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 5556 p.Gly106Ala missense_variant 0.11
gyrB 5720 p.Gly161Arg missense_variant 0.11
gyrB 5770 c.531C>A synonymous_variant 0.17
gyrB 6636 p.Ser466Cys missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491257 p.Gly159Arg missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576432 c.1087delC frameshift_variant 0.14
mshA 576547 p.Asp400Glu missense_variant 0.12
mshA 576566 p.Arg407Gly missense_variant 0.12
ccsA 619904 p.His5Arg missense_variant 0.12
ccsA 619978 p.Leu30Met missense_variant 0.25
ccsA 620041 c.153delC frameshift_variant 0.25
ccsA 620135 p.Ala82Asp missense_variant 0.33
ccsA 620224 p.Glu112* stop_gained 0.2
ccsA 620506 p.Pro206Thr missense_variant 0.19
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760835 p.His343Gln missense_variant 0.18
rpoB 760842 p.Gln346Lys missense_variant 0.17
rpoB 761016 c.1211delA frameshift_variant 0.17
rpoB 762760 p.Cys985Ser missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763905 p.Ala179Asp missense_variant 0.25
rpoC 763930 p.Glu187Asp missense_variant 0.14
rpoC 764108 p.Arg247Gly missense_variant 0.11
rpoC 765273 p.Val635Gly missense_variant 0.17
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 767225 p.Pro1286Thr missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775738 p.Leu915Val missense_variant 0.11
mmpL5 775757 c.2724C>A synonymous_variant 0.16
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 778090 p.Gly131Trp missense_variant 0.15
mmpS5 778839 p.Phe23Leu missense_variant 0.11
mmpL5 779280 c.-800G>C upstream_gene_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303140 c.210C>A synonymous_variant 0.22
Rv1258c 1406134 p.Leu403Met missense_variant 0.14
Rv1258c 1406727 p.Pro205His missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417167 p.Glu61Gln missense_variant 0.18
embR 1417203 p.Pro49Ala missense_variant 0.18
embR 1417285 p.Met21Ile missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472006 n.161G>T non_coding_transcript_exon_variant 0.22
rrs 1472530 n.685G>T non_coding_transcript_exon_variant 0.29
rrs 1472546 n.701G>T non_coding_transcript_exon_variant 0.15
rrs 1472549 n.704G>T non_coding_transcript_exon_variant 0.15
rrs 1472618 n.773A>G non_coding_transcript_exon_variant 0.11
rrs 1472698 n.853A>G non_coding_transcript_exon_variant 0.18
rrs 1472712 n.867G>T non_coding_transcript_exon_variant 0.18
rrs 1472722 n.878G>T non_coding_transcript_exon_variant 0.18
rrs 1473140 n.1295C>G non_coding_transcript_exon_variant 0.12
rrl 1473723 n.66C>A non_coding_transcript_exon_variant 0.25
rrl 1473848 n.191G>C non_coding_transcript_exon_variant 0.14
rrl 1474126 n.469G>T non_coding_transcript_exon_variant 0.33
rrl 1474185 n.528G>T non_coding_transcript_exon_variant 0.22
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.17
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.18
rrl 1474432 n.775C>A non_coding_transcript_exon_variant 0.18
rrl 1474610 n.953C>A non_coding_transcript_exon_variant 0.29
rrl 1474650 n.993G>T non_coding_transcript_exon_variant 0.29
rrl 1474907 n.1250C>A non_coding_transcript_exon_variant 0.22
rrl 1474999 n.1342C>A non_coding_transcript_exon_variant 0.22
rrl 1475324 n.1667G>A non_coding_transcript_exon_variant 0.17
rrl 1475543 n.1886G>T non_coding_transcript_exon_variant 0.22
rrl 1475820 n.2163C>G non_coding_transcript_exon_variant 0.13
rrl 1475998 n.2341C>A non_coding_transcript_exon_variant 0.15
rrl 1476466 n.2809C>A non_coding_transcript_exon_variant 0.29
fabG1 1673572 p.Thr45Ala missense_variant 0.11
inhA 1674779 p.Pro193His missense_variant 0.15
rpsA 1833959 p.Leu140Ile missense_variant 0.21
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834541 p.Pro334Thr missense_variant 0.21
tlyA 1917906 c.-33delC upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154436 p.Ala559Gly missense_variant 0.13
katG 2154445 p.Ala556Glu missense_variant 0.15
katG 2154468 c.1644C>A synonymous_variant 0.18
katG 2154473 p.Gly547Cys missense_variant 0.18
katG 2154522 c.1590C>A synonymous_variant 0.15
katG 2154557 p.Arg519Ser missense_variant 0.17
katG 2154567 c.1545C>A synonymous_variant 0.17
katG 2154572 p.Leu514Met missense_variant 0.15
katG 2154578 p.Gly512Arg missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154744 c.1368C>G synonymous_variant 0.13
katG 2154817 p.Pro432His missense_variant 0.22
katG 2155395 c.717G>C synonymous_variant 0.15
katG 2155737 c.375C>A synonymous_variant 0.19
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222259 c.906G>C synonymous_variant 0.12
Rv1979c 2222304 p.Asp287Glu missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289187 p.Leu19Met missense_variant 0.17
pncA 2289789 c.-548C>G upstream_gene_variant 0.11
kasA 2518248 p.Ala45Glu missense_variant 0.17
kasA 2518411 c.297C>G synonymous_variant 0.14
kasA 2518754 p.Arg214Trp missense_variant 0.17
eis 2715088 p.Leu82Pro missense_variant 0.25
folC 2746337 p.Ala421Asp missense_variant 0.19
pepQ 2859644 p.Ala259Ser missense_variant 0.16
pepQ 2860103 p.Gly106Arg missense_variant 0.12
pepQ 2860222 p.Ser66* stop_gained 0.22
ribD 2987069 c.231T>C synonymous_variant 0.17
ribD 2987073 p.Asp79Tyr missense_variant 0.17
ribD 2987327 p.Ile163Met missense_variant 0.11
ribD 2987387 c.549G>T synonymous_variant 0.19
thyX 3067423 c.522delG frameshift_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087921 p.Ser368Gly missense_variant 0.11
fbiD 3339314 p.Glu66Gly missense_variant 0.13
Rv3083 3448902 p.Cys133* stop_gained 0.21
Rv3083 3449079 p.Leu192Phe missense_variant 0.17
Rv3083 3449277 p.Cys258Trp missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612150 p.Gln323Glu missense_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640855 c.316delG frameshift_variant 0.12
fbiB 3642004 p.Arg157Leu missense_variant 0.2
fbiB 3642045 p.Ala171Ser missense_variant 0.18
fbiB 3642054 p.Arg174Ser missense_variant 0.15
fbiB 3642293 c.759C>G synonymous_variant 0.12
alr 3840361 p.Pro354Thr missense_variant 0.17
alr 3840760 p.Gln221Lys missense_variant 0.18
alr 3840766 p.Leu219Met missense_variant 0.22
rpoA 3878685 c.-178C>G upstream_gene_variant 0.15
clpC1 4038793 p.Leu638Met missense_variant 0.14
clpC1 4040270 p.Tyr145* stop_gained 0.14
clpC1 4040332 p.Val125Leu missense_variant 0.11
clpC1 4040377 c.327delG frameshift_variant 0.17
embC 4240531 p.Ser223Arg missense_variant 0.12
embC 4240701 p.Val280Glu missense_variant 0.2
embC 4240713 p.Trp284Leu missense_variant 0.25
embC 4240768 c.906G>T synonymous_variant 0.22
embA 4242439 c.-794G>A upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242938 p.Asp1026His missense_variant 0.13
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244184 p.Ser318Arg missense_variant 0.2
embA 4244223 p.Ala331Ser missense_variant 0.31
embA 4244984 p.Leu584Phe missense_variant 0.12
embA 4245601 p.Pro790His missense_variant 0.2
embB 4245614 c.-900C>T upstream_gene_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.11
embB 4246556 p.Ala15Pro missense_variant 0.11
embB 4247752 c.1239G>C synonymous_variant 0.15
embB 4247861 p.Ile450Val missense_variant 0.18
embB 4247894 p.Pro461Thr missense_variant 0.17
embB 4249289 p.Pro926Thr missense_variant 0.23
embB 4249352 c.2839C>A synonymous_variant 0.19
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268732 c.105G>C synonymous_variant 0.13
ethR 4326883 c.-666C>G upstream_gene_variant 0.15
ethA 4327554 c.-81G>T upstream_gene_variant 0.22
ethR 4327565 p.Ala6Asp missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408182 c.19_20delGC frameshift_variant 0.12