TB-Profiler result

Run: ERR9891960
Summary

Run ID: ERR9891960

Sample name:

Date: 02-04-2023 13:24:57

Number of reads: 1042820

Percentage reads mapped: 98.01

Strain: lineage4.1.2.1

Drug-resistance: Other

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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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491426 p.Ala215Asp missense_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575253 c.-95G>T upstream_gene_variant 0.13
mshA 575394 p.Arg16His missense_variant 0.14
mshA 575544 p.Gly66Val missense_variant 0.14
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575836 p.Trp163Cys missense_variant 0.2
mshA 576109 c.762G>A synonymous_variant 0.17
mshA 576705 p.Gln453Pro missense_variant 0.18
ccsA 620256 c.366C>A synonymous_variant 0.22
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760987 p.Val394Ala missense_variant 0.11
rpoB 761308 c.1505dupC frameshift_variant 0.12
rpoB 761644 p.Val613Ala missense_variant 0.11
rpoB 761659 p.Pro618Gln missense_variant 0.25
rpoB 762236 c.2430G>T synonymous_variant 0.12
rpoB 762418 p.Arg871Leu missense_variant 0.12
rpoC 762503 c.-867G>A upstream_gene_variant 0.12
rpoB 762708 p.Thr968Ala missense_variant 0.22
rpoC 763058 c.-312C>A upstream_gene_variant 0.11
rpoB 763060 p.Ile1085Asn missense_variant 0.11
rpoC 764330 p.Pro321Ser missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 0.94
rpoC 765305 p.Ile646Val missense_variant 0.11
rpoC 765901 c.2532G>T synonymous_variant 0.12
rpoC 766007 p.Val880Leu missense_variant 0.13
rpoC 766091 p.Gly908Ser missense_variant 0.15
rpoC 766265 p.Leu966Met missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775768 p.Gln905Lys missense_variant 0.4
mmpL5 775984 p.Trp833Arg missense_variant 0.12
mmpL5 776069 c.2412C>T synonymous_variant 0.12
mmpL5 777254 c.1227G>T synonymous_variant 0.2
mmpL5 777449 c.1032C>A synonymous_variant 0.2
mmpL5 777687 p.Leu265Arg missense_variant 0.12
mmpR5 779378 p.Pro130Leu missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303005 c.75G>A synonymous_variant 0.18
fbiC 1303024 c.97delG frameshift_variant 0.15
fbiC 1303245 p.Cys105Trp missense_variant 0.13
fbiC 1303875 c.945G>T synonymous_variant 0.22
fbiC 1303917 p.Met329Ile missense_variant 0.15
fbiC 1304261 p.Trp444Leu missense_variant 0.12
fbiC 1304371 p.His481Asn missense_variant 0.12
fbiC 1304401 p.Ile491Leu missense_variant 0.12
fbiC 1304421 c.1491C>A synonymous_variant 0.12
fbiC 1305193 p.Gly755Cys missense_variant 0.22
Rv1258c 1406083 c.1258T>A stop_lost&splice_region_variant 0.18
Rv1258c 1406404 p.Val313Ile missense_variant 0.13
Rv1258c 1406560 p.Gly261Cys missense_variant 0.13
Rv1258c 1406561 c.780G>T synonymous_variant 0.13
Rv1258c 1406709 p.Gly211Glu missense_variant 0.12
Rv1258c 1407492 c.-152C>A upstream_gene_variant 0.2
Rv1258c 1407515 c.-175G>T upstream_gene_variant 0.25
embR 1416750 p.Glu200* stop_gained 0.25
embR 1416939 p.His137Asn missense_variant 0.15
embR 1417192 c.156C>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674019 p.Leu194Met missense_variant 0.13
inhA 1674470 p.Gly90Val missense_variant 0.15
inhA 1674472 p.Val91Leu missense_variant 0.13
inhA 1674510 p.Met103Ile missense_variant 0.13
inhA 1674783 c.582C>A synonymous_variant 0.12
rpsA 1834327 c.786G>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918114 p.Glu59Gln missense_variant 0.18
tlyA 1918153 p.Gly72Cys missense_variant 0.25
tlyA 1918643 p.Gly235Val missense_variant 0.12
ndh 2101669 p.Ser458Arg missense_variant 0.14
ndh 2102104 c.939G>A synonymous_variant 0.12
ndh 2102139 c.904C>A synonymous_variant 0.12
ndh 2102362 p.Lys227Asn missense_variant 0.22
ndh 2102367 p.Ala226Pro missense_variant 0.29
ndh 2102754 p.Gln97Lys missense_variant 0.14
katG 2154482 p.Val544Phe missense_variant 0.17
katG 2154705 c.1407C>A synonymous_variant 0.12
katG 2155625 p.Asp163Tyr missense_variant 0.14
katG 2155795 p.Ala106Glu missense_variant 0.29
PPE35 2170066 p.Ala183Thr missense_variant 0.12
PPE35 2170204 p.Glu137* stop_gained 0.12
PPE35 2170283 c.330G>C synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518280 p.Leu56Ile missense_variant 0.12
kasA 2518788 p.Arg225Leu missense_variant 0.2
kasA 2519044 c.930G>T synonymous_variant 0.13
kasA 2519161 c.1047G>T synonymous_variant 0.15
eis 2714387 p.Glu316Lys missense_variant 0.2
eis 2714518 p.Gln272Pro missense_variant 0.11
eis 2714921 p.His138Tyr missense_variant 0.17
eis 2715491 c.-159G>A upstream_gene_variant 0.14
folC 2746187 p.Ser471* stop_gained 0.17
folC 2746447 p.Asp384Glu missense_variant 0.14
folC 2746557 p.Val348Leu missense_variant 0.2
folC 2746559 p.Thr347Met missense_variant 0.2
folC 2747519 c.79delC frameshift_variant 0.2
pepQ 2859716 p.Arg235Ser missense_variant 0.18
pepQ 2859829 p.Gly197Val missense_variant 0.15
pepQ 2860107 c.312G>T synonymous_variant 0.2
ribD 2987161 p.Ala108Val missense_variant 0.5
ribD 2987511 p.Arg225Ser missense_variant 0.2
Rv2752c 3064698 c.1494C>A synonymous_variant 0.14
Rv2752c 3064794 c.1398C>A synonymous_variant 0.14
Rv2752c 3065048 c.1144C>T synonymous_variant 0.13
Rv2752c 3065786 p.His136Asn missense_variant 0.18
Rv2752c 3066115 p.Glu26Gly missense_variant 0.11
Rv2752c 3066235 c.-44C>T upstream_gene_variant 0.14
Rv2752c 3066295 c.-104C>A upstream_gene_variant 0.17
thyX 3067662 p.Arg95Leu missense_variant 0.14
thyX 3068118 c.-173C>A upstream_gene_variant 0.14
thyA 3074428 p.Gly15Val missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 0.18
ald 3087862 p.Gly348Val missense_variant 0.12
fbiD 3338945 c.-173C>A upstream_gene_variant 0.14
fbiD 3339037 c.-81C>A upstream_gene_variant 0.22
Rv3083 3448318 c.-186G>T upstream_gene_variant 0.15
Rv3083 3449617 p.Thr372Ser missense_variant 0.17
Rv3083 3449646 c.1143C>T synonymous_variant 0.17
Rv3083 3449709 c.1206C>T synonymous_variant 0.17
Rv3083 3449867 p.Gly455Val missense_variant 0.17
fprA 3473809 c.-198G>A upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474153 c.147G>T synonymous_variant 0.12
fprA 3474257 p.Val84Asp missense_variant 0.12
fprA 3474503 p.Leu166Gln missense_variant 0.12
fprA 3474649 p.Leu215Met missense_variant 0.22
fprA 3474663 c.657C>T synonymous_variant 0.15
fprA 3474773 p.Ala256Glu missense_variant 0.22
fprA 3475182 c.1176C>T synonymous_variant 0.25
fprA 3475307 p.Gly434Val missense_variant 0.17
whiB7 3568427 p.Arg85Cys missense_variant 0.25
whiB7 3568796 c.-117G>A upstream_gene_variant 0.25
Rv3236c 3612097 c.1020C>A synonymous_variant 0.2
Rv3236c 3612935 p.Gly61Val missense_variant 0.17
fbiB 3640914 c.-621C>A upstream_gene_variant 0.17
fbiA 3640915 p.Leu125Met missense_variant 0.2
fbiA 3641276 p.Pro245Arg missense_variant 0.12
fbiB 3641725 p.Pro64His missense_variant 0.22
fbiB 3641854 p.Gly107Val missense_variant 0.17
fbiB 3641939 c.405G>C synonymous_variant 0.2
fbiB 3642698 c.1164G>T synonymous_variant 0.12
rpoA 3877813 p.Ile232Asn missense_variant 0.13
clpC1 4038693 p.Ser671Phe missense_variant 0.15
clpC1 4038927 p.Arg593Leu missense_variant 0.13
clpC1 4039009 p.Leu566Met missense_variant 0.22
clpC1 4039074 p.Arg544Leu missense_variant 0.13
clpC1 4040050 p.Gly219Cys missense_variant 0.17
clpC1 4040308 c.397C>A synonymous_variant 0.2
embC 4239883 c.21A>G synonymous_variant 0.13
embC 4239907 c.45A>T synonymous_variant 0.13
embC 4240004 p.Pro48Thr missense_variant 0.2
embC 4240108 c.246G>A synonymous_variant 0.13
embC 4240133 p.Ala91Ser missense_variant 0.18
embC 4240319 p.Gln153Lys missense_variant 0.17
embC 4240350 p.Arg163Leu missense_variant 0.22
embC 4240409 p.Pro183Ala missense_variant 0.12
embC 4240863 p.Trp334* stop_gained 0.12
embC 4240975 c.1113C>A synonymous_variant 0.14
embC 4241581 c.1719C>A synonymous_variant 0.13
embC 4241905 c.2043C>T synonymous_variant 0.15
embC 4242071 p.Gly737Cys missense_variant 0.17
embC 4242296 p.Asp812Tyr missense_variant 0.33
embC 4242421 p.Ser853Arg missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242773 p.Leu971Met missense_variant 0.22
embC 4242781 c.2920delG frameshift_variant 0.22
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242891 p.Arg1010Gln missense_variant 0.17
embC 4242974 p.Leu1038Met missense_variant 0.2
embA 4243572 p.Val114Phe missense_variant 0.4
embA 4243600 p.Ala123Asp missense_variant 0.5
embA 4243660 p.Ala143Asp missense_variant 0.22
embA 4243682 c.450T>C synonymous_variant 0.17
embA 4246111 p.Arg960Leu missense_variant 0.15
embA 4246285 p.Ser1018Trp missense_variant 0.18
embB 4246896 p.Arg128His missense_variant 0.14
embB 4246979 p.Gly156Ser missense_variant 0.13
embB 4248023 p.Glu504* stop_gained 0.17
embB 4248041 p.Ala510Ser missense_variant 0.12
embB 4248537 p.Leu675Pro missense_variant 0.12
embB 4249634 p.Asp1041Asn missense_variant 0.2
aftB 4267735 p.Gly368Ser missense_variant 0.12
aftB 4268220 p.Thr206Asn missense_variant 0.17
aftB 4268390 c.447G>T synonymous_variant 0.5
ubiA 4269167 p.Thr223Ser missense_variant 0.13
ubiA 4269373 p.Ser154* stop_gained 0.14
ethR 4326868 c.-681G>A upstream_gene_variant 0.12
ethA 4327108 p.Ser122Arg missense_variant 0.13
ethR 4327429 c.-120G>A upstream_gene_variant 0.12
ethA 4328301 c.-828C>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0