TB-Profiler result

Run: ERR2229659
Summary

Run ID: ERR2229659

Sample name:

Date: 31-03-2023 17:24:20

Number of reads: 879578

Percentage reads mapped: 99.2

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gyrB 6663 p.Phe475Ser missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8874 p.Tyr525His missense_variant 0.11
gyrA 9400 p.Val700Ala missense_variant 0.1
fgd1 490962 c.180T>A synonymous_variant 0.13
fgd1 491149 p.Pro123Thr missense_variant 0.12
mshA 575356 c.9T>A synonymous_variant 0.2
mshA 575545 c.198C>T synonymous_variant 0.18
mshA 576386 p.Ala347Thr missense_variant 0.17
ccsA 620785 p.Gly299Ser missense_variant 0.12
rpoB 760507 p.Ala234Val missense_variant 0.18
rpoB 760511 c.705G>A synonymous_variant 0.15
rpoB 760666 p.Gln287Arg missense_variant 0.15
rpoB 761372 c.1566C>T synonymous_variant 0.15
rpoB 761941 p.Asn712Ser missense_variant 0.13
rpoB 761982 p.Glu726Lys missense_variant 0.14
rpoB 762753 p.Leu983Met missense_variant 0.14
rpoB 763080 p.Gly1092Cys missense_variant 0.11
rpoC 763986 p.Arg206His missense_variant 0.18
rpoC 764649 p.Arg427Gln missense_variant 0.12
rpoC 764654 p.Val429Phe missense_variant 0.13
rpoC 766118 p.Glu917* stop_gained 0.22
rpoC 766330 p.Lys987Asn missense_variant 0.12
mmpL5 775599 p.Phe961Cys missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775732 p.Asp917Asn missense_variant 0.13
mmpL5 775971 p.Ala837Glu missense_variant 0.14
mmpL5 776330 c.2151G>T synonymous_variant 0.12
mmpR5 779320 p.Met111Leu missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800667 c.-142_-140delTCGinsAGC upstream_gene_variant 0.14
rplC 800672 c.-137G>C upstream_gene_variant 0.14
rplC 800693 c.-116A>G upstream_gene_variant 0.14
rplC 800703 c.-106T>C upstream_gene_variant 0.11
rplC 801194 p.Arg129Gln missense_variant 0.13
fbiC 1303003 p.Ala25Ser missense_variant 0.14
fbiC 1303021 p.Arg31* stop_gained 0.17
fbiC 1303062 c.132G>T synonymous_variant 0.22
fbiC 1303507 p.Pro193Ser missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406324 c.1017G>T synonymous_variant 0.18
Rv1258c 1407144 p.Val66Ala missense_variant 0.11
embR 1416708 p.Ala214Thr missense_variant 0.29
embR 1417158 p.Pro64Ala missense_variant 0.11
embR 1417513 c.-166A>G upstream_gene_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472806 n.961A>G non_coding_transcript_exon_variant 0.13
rrl 1473429 n.-229G>T upstream_gene_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474042 n.385G>A non_coding_transcript_exon_variant 0.25
rrl 1474549 n.892G>A non_coding_transcript_exon_variant 0.33
rrl 1474619 n.962G>T non_coding_transcript_exon_variant 0.25
rrl 1475694 n.2037A>T non_coding_transcript_exon_variant 0.4
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673349 c.-91G>C upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.24
fabG1 1673512 c.78dupG frameshift_variant 0.2
fabG1 1674083 p.Ala215Val missense_variant 0.22
inhA 1674093 c.-109C>T upstream_gene_variant 0.18
rpsA 1833395 c.-147C>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154645 c.1467C>T synonymous_variant 0.33
katG 2154803 c.1309C>T synonymous_variant 0.18
katG 2155009 p.Phe368Ser missense_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169017 c.1596G>A synonymous_variant 0.13
PPE35 2169269 c.1344A>G synonymous_variant 0.11
PPE35 2169278 c.1335T>C synonymous_variant 0.18
PPE35 2169281 c.1332T>G synonymous_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.59
PPE35 2170053 p.Thr187Ser missense_variant 0.6
PPE35 2170125 p.Val163Glu missense_variant 0.14
PPE35 2170159 p.Ala152Ser missense_variant 0.12
PPE35 2170371 p.Thr81Val missense_variant 0.24
PPE35 2170385 c.228G>T synonymous_variant 0.24
PPE35 2170392 p.Gly74Ala missense_variant 0.25
PPE35 2170400 c.213G>C synonymous_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518213 p.Trp33Cys missense_variant 0.33
kasA 2519017 c.903G>T synonymous_variant 0.18
eis 2714617 p.Ser239Asn missense_variant 0.14
eis 2715463 c.-131C>A upstream_gene_variant 0.12
folC 2746648 c.951G>A synonymous_variant 0.22
folC 2747561 p.Ser13* stop_gained 0.12
ald 3087324 p.Ala169Ser missense_variant 0.29
ald 3087410 c.591A>G synonymous_variant 0.18
Rv3083 3448333 c.-171G>T upstream_gene_variant 0.22
fprA 3474245 p.Gly80Val missense_variant 0.18
fprA 3474786 c.780C>A synonymous_variant 0.14
Rv3236c 3612916 c.201G>T synonymous_variant 0.22
Rv3236c 3613033 c.84C>T synonymous_variant 0.29
fbiB 3640701 c.-834C>A upstream_gene_variant 0.14
fbiB 3641891 c.357G>A synonymous_variant 0.12
alr 3840365 c.1056C>G synonymous_variant 0.15
rpoA 3877961 p.Val183Phe missense_variant 0.18
rpoA 3878406 c.102G>T synonymous_variant 0.11
clpC1 4039645 p.His354Asp missense_variant 0.14
clpC1 4039730 c.975C>G synonymous_variant 0.14
clpC1 4040251 p.Glu152Lys missense_variant 0.2
clpC1 4040253 p.Ala151Asp missense_variant 0.2
panD 4043958 c.324C>A synonymous_variant 0.15
embC 4240171 c.309G>T synonymous_variant 0.11
embC 4240746 p.Gly295Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244284 c.1055delG frameshift_variant 0.33
embA 4246145 c.2916delG frameshift_variant 0.12
embA 4246180 p.Thr983Ile missense_variant 0.18
embB 4246337 c.-177G>T upstream_gene_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.38
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4246951 c.438A>G synonymous_variant 0.15
embB 4249461 p.Pro983Leu missense_variant 0.18
embB 4249708 c.3195C>T synonymous_variant 0.25
aftB 4268891 c.-55G>T upstream_gene_variant 0.22
ethR 4326961 c.-588G>C upstream_gene_variant 0.13
ethR 4326964 c.-585G>A upstream_gene_variant 0.13
ethR 4326970 c.-579G>T upstream_gene_variant 0.12
ethR 4327672 p.Leu42Met missense_variant 0.14
ethR 4327699 p.Ala51Ser missense_variant 0.12
ethA 4328395 c.-923_-922insA upstream_gene_variant 0.12
ethA 4328400 c.-927C>T upstream_gene_variant 0.14
whiB6 4338363 p.Cys53* stop_gained 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407712 p.Gly164Val missense_variant 0.15
gid 4407731 p.Arg158* stop_gained 0.14
gid 4407917 p.Arg96Ser missense_variant 0.12
gid 4408108 p.Glu32Gly missense_variant 0.11
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0