TB-Profiler result

Run: ERR3994095
Summary

Run ID: ERR3994095

Sample name:

Date: 01-04-2023 03:42:26

Number of reads: 3113714

Percentage reads mapped: 99.98

Strain: lineage4.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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
katG 2154234 c.1877delT frameshift_variant 0.11 isoniazid
ethA 4326160 c.1313delA frameshift_variant 0.12 ethionamide
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 5492 p.Pro85Ala missense_variant 0.11
gyrB 5733 p.Lys165Arg missense_variant 0.17
gyrB 5832 p.Ala198Glu missense_variant 0.14
gyrB 5903 p.Val222Leu missense_variant 0.11
gyrB 6355 p.Lys372Asn missense_variant 0.17
gyrB 6463 p.Asn408Lys missense_variant 0.11
gyrA 7264 c.-38C>G upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7709 c.408G>A synonymous_variant 0.15
gyrA 7794 p.Val165Met missense_variant 0.17
gyrA 7890 c.589C>T synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575652 p.Arg102Pro missense_variant 0.29
mshA 575681 p.Val112Met missense_variant 0.2
mshA 575740 c.393G>T synonymous_variant 0.15
mshA 576586 c.1239G>C synonymous_variant 0.67
ccsA 619761 c.-130G>T upstream_gene_variant 0.12
ccsA 619995 p.Glu35Asp missense_variant 0.12
ccsA 620082 c.192G>C synonymous_variant 0.25
ccsA 620457 c.567C>G synonymous_variant 0.15
ccsA 620654 p.Trp255Ser missense_variant 0.12
ccsA 620783 p.Ala298Asp missense_variant 0.2
rpoB 759921 p.Arg39Gly missense_variant 0.12
rpoB 760990 p.Arg395Gln missense_variant 0.29
rpoB 761922 p.Glu706Gln missense_variant 0.12
rpoB 762122 p.Asp772Glu missense_variant 0.11
rpoB 762219 p.Glu805Lys missense_variant 0.22
rpoB 762418 p.Arg871His missense_variant 0.12
rpoB 762447 p.Gly881Ser missense_variant 0.13
rpoC 762485 c.-885G>A upstream_gene_variant 0.17
rpoB 762931 p.Pro1042Arg missense_variant 0.12
rpoC 763684 p.Trp105* stop_gained 0.11
rpoC 763701 p.Pro111Leu missense_variant 0.11
rpoC 764015 c.646C>T synonymous_variant 0.2
rpoC 764167 c.798G>A synonymous_variant 0.12
rpoC 764185 c.816C>A synonymous_variant 0.12
rpoC 764801 p.Arg478Gly missense_variant 0.29
rpoC 765036 p.Arg556His missense_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765705 p.Lys779Thr missense_variant 0.14
rpoC 765949 c.2580G>A synonymous_variant 0.25
rpoC 766151 p.Asp928His missense_variant 0.11
rpoC 766333 c.2964G>A synonymous_variant 0.18
rpoC 766503 p.Pro1045Leu missense_variant 0.12
rpoC 766521 p.Gly1051Val missense_variant 0.12
rpoC 766549 c.3180G>C synonymous_variant 0.11
rpoC 766584 p.Gly1072Ala missense_variant 0.11
rpoC 766802 p.Gln1145Glu missense_variant 0.25
rpoC 766884 p.Ser1172Trp missense_variant 0.29
rpoC 766940 p.Arg1191Gly missense_variant 0.4
rpoC 767143 c.3774C>A synonymous_variant 0.13
rpoC 767237 p.Asp1290Tyr missense_variant 0.12
rpoC 767238 c.3870delT frameshift_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777016 p.Gly489Cys missense_variant 0.14
mmpL5 777034 p.Ala483Pro missense_variant 0.15
mmpL5 777213 p.Ala423Gly missense_variant 0.11
mmpL5 777461 c.1020G>C synonymous_variant 0.14
mmpL5 777784 c.697C>T synonymous_variant 0.14
mmpL5 778747 c.-267C>A upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781505 c.-55G>C upstream_gene_variant 0.15
rplC 800972 p.Gly55Ala missense_variant 0.12
rplC 801241 p.His145Asp missense_variant 0.1
fbiC 1303259 p.Val110Ala missense_variant 0.18
fbiC 1303265 p.Gly112Ala missense_variant 0.18
fbiC 1303413 p.Trp161Cys missense_variant 0.14
fbiC 1303437 c.507C>A synonymous_variant 0.13
fbiC 1303537 c.607C>A synonymous_variant 0.18
fbiC 1303924 p.Gln332Lys missense_variant 0.15
fbiC 1303944 c.1014G>A synonymous_variant 0.17
fbiC 1304798 p.Ala623Gly missense_variant 0.15
fbiC 1305232 p.Ala768Pro missense_variant 0.18
fbiC 1305307 p.Val793Leu missense_variant 0.17
fbiC 1305439 p.Ala837Thr missense_variant 0.17
Rv1258c 1406685 c.655delG frameshift_variant 0.22
Rv1258c 1406775 p.Ala189Val missense_variant 0.29
embR 1416314 p.Arg345Pro missense_variant 0.12
embR 1416393 c.953_954delTC frameshift_variant 0.2
atpE 1460954 c.-91G>A upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.19
rrs 1473023 n.1178G>T non_coding_transcript_exon_variant 0.4
rrs 1473060 n.1215C>A non_coding_transcript_exon_variant 0.2
rrs 1473086 n.1241C>A non_coding_transcript_exon_variant 0.14
rrl 1474376 n.719T>A non_coding_transcript_exon_variant 0.12
rrl 1474383 n.726G>A non_coding_transcript_exon_variant 0.12
rrl 1474499 n.842G>A non_coding_transcript_exon_variant 0.11
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.14
rrl 1475265 n.1608G>A non_coding_transcript_exon_variant 1.0
rrl 1476262 n.2605G>C non_coding_transcript_exon_variant 0.1
inhA 1674556 p.Gly119Arg missense_variant 0.15
inhA 1674959 p.Thr253Ile missense_variant 0.2
rpsA 1833554 p.Thr5Ala missense_variant 0.15
rpsA 1833737 p.Arg66Cys missense_variant 0.12
rpsA 1833765 c.228dupC frameshift_variant 0.12
rpsA 1834482 p.Glu314Gly missense_variant 0.14
rpsA 1834538 p.Val333Met missense_variant 0.12
rpsA 1834774 c.1233C>G synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918346 p.Ala136Glu missense_variant 0.12
tlyA 1918581 c.642G>C synonymous_variant 0.17
tlyA 1918726 p.Ala263Pro missense_variant 0.5
ndh 2101878 p.Gly389Arg missense_variant 0.11
ndh 2103207 c.-165C>A upstream_gene_variant 0.15
katG 2154618 c.1494C>T synonymous_variant 0.12
katG 2155324 p.Ala263Glu missense_variant 0.13
katG 2155847 p.Pro89Ala missense_variant 0.18
katG 2156230 c.-119C>A upstream_gene_variant 0.13
katG 2156307 c.-196T>C upstream_gene_variant 0.12
katG 2156498 c.-388dupC upstream_gene_variant 0.13
katG 2156501 c.-390C>A upstream_gene_variant 0.13
PPE35 2167718 p.Ser965Arg missense_variant 0.11
PPE35 2170102 p.Pro171Ala missense_variant 0.15
PPE35 2170384 p.Ala77Thr missense_variant 0.22
PPE35 2170604 p.Tyr3* stop_gained 0.18
PPE35 2170631 c.-19C>G upstream_gene_variant 0.18
PPE35 2170663 c.-52delC upstream_gene_variant 0.12
Rv1979c 2222499 c.666G>C synonymous_variant 0.15
Rv1979c 2222502 p.Met221Ile missense_variant 0.15
Rv1979c 2222517 c.648C>G synonymous_variant 0.25
Rv1979c 2222870 p.Ala99Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289006 p.Ala79Val missense_variant 0.18
kasA 2518677 p.Gly188Ala missense_variant 0.29
kasA 2518757 p.Ala215Thr missense_variant 0.4
eis 2714224 p.Ala370Gly missense_variant 0.15
eis 2714304 c.1029C>G synonymous_variant 0.14
eis 2714458 p.Asp292Gly missense_variant 0.12
eis 2714862 c.471C>T synonymous_variant 0.2
eis 2715145 p.Leu63Pro missense_variant 0.29
eis 2715413 c.-81G>C upstream_gene_variant 0.25
ahpC 2726210 c.18T>C synonymous_variant 1.0
folC 2747260 p.Lys113Asn missense_variant 0.22
folC 2747264 p.Gly112Ala missense_variant 0.22
folC 2747434 p.Asp55Glu missense_variant 0.25
pepQ 2859381 c.1038C>T synonymous_variant 0.12
pepQ 2859404 p.Glu339* stop_gained 0.12
pepQ 2859738 c.681C>G synonymous_variant 0.22
pepQ 2859864 c.555T>C synonymous_variant 0.17
pepQ 2859926 p.Pro165Ala missense_variant 0.22
pepQ 2859992 p.Leu143Val missense_variant 0.22
pepQ 2860131 c.288C>G synonymous_variant 0.18
pepQ 2860263 c.156C>G synonymous_variant 0.14
ribD 2987015 p.Ser59Arg missense_variant 0.18
ribD 2987572 p.Thr245Asn missense_variant 0.22
ribD 2987594 p.Tyr252* stop_gained 0.2
Rv2752c 3064764 c.1428C>G synonymous_variant 0.13
Rv2752c 3065006 p.Val396Leu missense_variant 0.11
Rv2752c 3065203 p.Ala330Gly missense_variant 0.11
Rv2752c 3065731 p.Leu154Ser missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086806 c.-14C>A upstream_gene_variant 0.12
fbiD 3339514 p.Arg133Ser missense_variant 0.25
Rv3083 3448512 p.Gln3His missense_variant 0.12
Rv3083 3448901 p.Cys133Ser missense_variant 0.4
Rv3083 3449323 p.Arg274* stop_gained 0.17
Rv3083 3449363 p.Thr287Ile missense_variant 0.13
fprA 3473844 c.-163A>G upstream_gene_variant 0.2
fprA 3473874 c.-133_-132insG upstream_gene_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474192 c.186G>A synonymous_variant 0.12
fprA 3474322 p.Ala106Arg missense_variant 0.17
fprA 3474366 c.360G>A synonymous_variant 0.17
fprA 3474681 c.675C>T synonymous_variant 0.12
fprA 3475327 c.1321C>A synonymous_variant 0.17
whiB7 3568404 c.276A>T synonymous_variant 0.25
Rv3236c 3612140 p.Ala326Val missense_variant 0.22
Rv3236c 3612520 c.597G>A synonymous_variant 0.17
Rv3236c 3612703 c.414G>A synonymous_variant 0.2
fbiA 3640693 p.Ala51Pro missense_variant 0.22
fbiA 3640753 p.Gly71Pro missense_variant 0.17
fbiA 3640828 p.Gly96Ser missense_variant 0.12
fbiA 3640973 p.Pro144Arg missense_variant 0.22
fbiA 3641039 p.Ala166Gly missense_variant 0.22
fbiA 3641063 p.Val174Glu missense_variant 0.29
fbiB 3641316 c.-219G>A upstream_gene_variant 0.29
fbiA 3641447 p.Thr302Met missense_variant 1.0
fbiB 3642111 p.Ala193Thr missense_variant 0.33
alr 3840514 p.Arg303Cys missense_variant 0.13
alr 3841312 p.Glu37Gln missense_variant 0.17
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3877559 p.Pro317Ser missense_variant 0.12
rpoA 3877731 c.775_776dupCG frameshift_variant 0.12
rpoA 3878027 p.Arg161Ser missense_variant 0.14
ddn 3986742 c.-102G>C upstream_gene_variant 0.12
ddn 3987012 p.Gly57Ser missense_variant 0.14
ddn 3987022 p.Arg60Leu missense_variant 0.18
ddn 3987045 p.Arg68Cys missense_variant 0.2
clpC1 4038542 p.Gln721His missense_variant 0.18
clpC1 4038666 p.Gly680Asp missense_variant 0.2
clpC1 4039736 c.969C>T synonymous_variant 0.12
clpC1 4039806 p.Gly300Ala missense_variant 0.13
clpC1 4039820 c.885T>C synonymous_variant 0.12
clpC1 4039898 c.807C>A synonymous_variant 0.17
clpC1 4040344 p.Ala121Pro missense_variant 0.11
clpC1 4040447 p.Lys86Asn missense_variant 0.14
clpC1 4040786 c.-82G>C upstream_gene_variant 0.13
panD 4043993 p.Arg97Trp missense_variant 0.14
panD 4044204 c.78G>T synonymous_variant 0.25
panD 4044414 c.-133G>C upstream_gene_variant 0.29
embC 4239830 c.-33G>T upstream_gene_variant 0.12
embC 4240343 p.Ala161Ser missense_variant 0.13
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4241428 c.1566G>T synonymous_variant 0.2
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242855 p.Gly998Asp missense_variant 0.22
embA 4244163 p.Leu311Ile missense_variant 0.17
embA 4244487 p.Ala419Thr missense_variant 0.4
embA 4245076 p.Ala615Gly missense_variant 0.4
embA 4245353 p.Lys707Asn missense_variant 0.25
embB 4245716 c.-798G>C upstream_gene_variant 0.33
embB 4246028 c.-486G>A upstream_gene_variant 0.22
embA 4246038 p.Ala936Thr missense_variant 0.22
embB 4246490 c.-24G>A upstream_gene_variant 0.22
embB 4247037 p.Gly175Asp missense_variant 0.29
embB 4247878 c.1365G>C synonymous_variant 0.67
embB 4248224 p.Ala571Thr missense_variant 0.13
embB 4248673 c.2160G>A synonymous_variant 0.14
embB 4248894 p.Pro794Arg missense_variant 0.18
embB 4249002 p.Thr830Met missense_variant 0.2
embB 4249141 c.2630_2631dupTG frameshift_variant&stop_gained 0.2
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249517 p.His1002Asp missense_variant 0.18
embB 4249557 p.Thr1015Lys missense_variant 0.17
aftB 4267528 p.Ala437Pro missense_variant 0.11
aftB 4267953 p.Ala295Val missense_variant 0.33
aftB 4268544 p.Leu98Pro missense_variant 0.5
aftB 4268603 c.234C>A synonymous_variant 0.29
aftB 4268726 c.111G>T synonymous_variant 0.18
aftB 4269393 c.-557G>C upstream_gene_variant 0.12
ethA 4326118 c.1356T>C synonymous_variant 0.11
ethR 4326595 c.-954C>T upstream_gene_variant 0.17
ethR 4326997 c.-552C>G upstream_gene_variant 0.18
ethA 4327028 p.Pro149Gln missense_variant 0.17
ethA 4327091 p.Ala128Val missense_variant 0.15
ethR 4327342 c.-207G>T upstream_gene_variant 0.17
ethR 4327676 p.Ala43Gly missense_variant 0.17
ethA 4328281 c.-808C>G upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408418 c.-216C>A upstream_gene_variant 0.25
gid 4408456 c.-254C>G upstream_gene_variant 1.0