TB-Profiler result

Run: ERR4819687
Summary

Run ID: ERR4819687

Sample name:

Date: 01-04-2023 16:15:02

Number of reads: 609000

Percentage reads mapped: 95.43

Strain: lineage1.2.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.99
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 1472750 n.905C>G non_coding_transcript_exon_variant 0.56 streptomycin
katG 2154391 p.Ala574Val missense_variant 0.67 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 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 5151 c.-89C>G upstream_gene_variant 0.2
gyrB 5247 p.Ala3Val missense_variant 0.17
gyrB 5387 p.Val50Phe missense_variant 0.33
gyrB 5908 c.669C>T synonymous_variant 0.4
gyrB 6092 p.His285Asn missense_variant 0.25
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6495 p.Ala419Val missense_variant 0.22
gyrB 6817 p.Lys526Asn missense_variant 0.4
gyrB 7019 p.Gly594Trp missense_variant 0.17
gyrB 7027 p.Lys596Asn missense_variant 0.15
gyrA 7033 c.-269G>T upstream_gene_variant 0.17
gyrB 7211 p.Ala658Thr missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7511 c.210C>T synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7986 p.Pro229Ser missense_variant 0.15
gyrA 8240 c.939C>T synonymous_variant 0.18
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.91
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490784 p.Val1Ala missense_variant 0.18
fgd1 491071 p.Tyr97His missense_variant 0.29
fgd1 491451 c.669C>T synonymous_variant 0.4
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575623 c.276C>T synonymous_variant 0.17
mshA 575633 p.Ala96Thr missense_variant 0.17
mshA 575915 p.Asp190Tyr missense_variant 0.12
mshA 576035 p.Ala230Ser missense_variant 0.14
mshA 576431 p.Ala362Thr missense_variant 0.13
ccsA 620118 c.228C>A synonymous_variant 0.22
ccsA 620211 p.Trp107Cys missense_variant 0.33
ccsA 620769 c.879C>A synonymous_variant 0.25
rpoB 759855 p.Arg17Cys missense_variant 0.33
rpoB 760853 p.Met349Ile missense_variant 0.12
rpoB 760865 c.1059C>A synonymous_variant 0.12
rpoB 761396 p.Glu530Asp missense_variant 0.14
rpoB 761786 c.1980C>T synonymous_variant 0.17
rpoB 762405 p.Val867Leu missense_variant 0.17
rpoC 762896 c.-474G>A upstream_gene_variant 0.18
rpoC 762926 c.-444C>A upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763492 c.123G>T synonymous_variant 0.22
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765174 p.Ala602Asp missense_variant 0.15
rpoC 765500 p.Gln711* stop_gained 0.33
rpoC 765682 p.Asn771Lys missense_variant 0.25
rpoC 765929 p.His854Asn missense_variant 0.22
rpoC 766459 c.3090G>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775746 p.Met912Thr missense_variant 1.0
mmpL5 776083 p.Ala800Ser missense_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776320 p.Ser721Cys missense_variant 0.5
mmpL5 778504 c.-24G>A upstream_gene_variant 0.18
mmpS5 778577 p.Thr110Ile missense_variant 0.14
rpsL 781385 c.-175C>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801196 p.His130Tyr missense_variant 0.13
rplC 801335 p.Thr176Asn missense_variant 0.12
fbiC 1303017 c.87A>T synonymous_variant 0.2
fbiC 1303467 c.537C>T synonymous_variant 0.17
fbiC 1303526 p.Ser199Leu missense_variant 0.17
fbiC 1304014 p.Pro362Asn missense_variant 0.12
fbiC 1304129 p.Gln400Leu missense_variant 0.25
fbiC 1304416 p.Leu496Phe missense_variant 0.15
fbiC 1304544 c.1614T>C synonymous_variant 0.29
fbiC 1304996 p.Leu689Ser missense_variant 0.13
fbiC 1305105 c.2175G>T synonymous_variant 0.12
Rv1258c 1406296 p.Val349Phe missense_variant 0.22
Rv1258c 1406554 p.Ala263Ser missense_variant 0.25
Rv1258c 1407261 p.Ile27Thr missense_variant 0.22
embR 1416331 c.1017C>T synonymous_variant 0.29
embR 1416457 c.891G>A synonymous_variant 0.15
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417403 c.-56G>T upstream_gene_variant 0.18
atpE 1460853 c.-192T>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471878 n.33C>T non_coding_transcript_exon_variant 0.25
rrs 1471955 n.110G>A non_coding_transcript_exon_variant 0.2
rrs 1472469 n.624G>T non_coding_transcript_exon_variant 0.25
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.2
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.29
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.44
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.36
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.44
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.44
rrl 1473458 n.-200G>T upstream_gene_variant 0.4
rrl 1473596 n.-62G>C upstream_gene_variant 0.18
rrl 1473766 n.109G>T non_coding_transcript_exon_variant 0.29
rrl 1474317 n.660G>A non_coding_transcript_exon_variant 0.2
rrl 1474640 n.983C>T non_coding_transcript_exon_variant 0.18
rrl 1474768 n.1111C>T non_coding_transcript_exon_variant 0.18
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.2
rrl 1474809 n.1152T>A non_coding_transcript_exon_variant 0.13
rrl 1475209 n.1552G>A non_coding_transcript_exon_variant 0.5
rrl 1475310 n.1653A>G non_coding_transcript_exon_variant 0.18
rrl 1476117 n.2460G>T non_coding_transcript_exon_variant 0.5
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.4
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.44
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.57
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.4
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476482 n.2825A>G non_coding_transcript_exon_variant 0.2
fabG1 1673341 c.-99T>C upstream_gene_variant 0.17
fabG1 1673657 p.Thr73Met missense_variant 0.25
inhA 1674454 p.Gly85Cys missense_variant 0.25
inhA 1674687 c.486G>A synonymous_variant 0.13
inhA 1674956 p.Ala252Glu missense_variant 0.25
rpsA 1833431 c.-111T>G upstream_gene_variant 0.2
rpsA 1833636 p.Tyr32Cys missense_variant 0.12
rpsA 1833688 p.Asp49Glu missense_variant 0.12
rpsA 1834008 p.Arg156Pro missense_variant 0.2
rpsA 1834054 c.513C>A synonymous_variant 0.13
rpsA 1834717 p.Phe392Leu missense_variant 0.17
tlyA 1917768 c.-172C>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918435 p.Ala166Ser missense_variant 0.22
ndh 2101807 c.1236C>T synonymous_variant 0.25
ndh 2102307 p.Gly246Cys missense_variant 0.5
ndh 2102465 p.Ala193Tyr missense_variant 0.2
ndh 2103140 c.-98G>A upstream_gene_variant 0.18
katG 2154519 c.1593G>A synonymous_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154731 p.Gln461Lys missense_variant 0.33
katG 2155008 p.Phe368Leu missense_variant 0.14
katG 2155879 p.Arg78Leu missense_variant 0.17
katG 2155955 p.Ala53Ser missense_variant 0.2
katG 2156281 c.-170C>A upstream_gene_variant 0.2
katG 2156515 c.-404G>A upstream_gene_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168071 p.Glu848Lys missense_variant 0.17
PPE35 2168533 p.Val694Leu missense_variant 1.0
PPE35 2169240 p.Pro458His missense_variant 0.25
PPE35 2169899 c.714G>T synonymous_variant 0.2
PPE35 2170465 p.Ala50Thr missense_variant 0.22
PPE35 2170527 p.Ser29Val missense_variant 0.18
PPE35 2170544 c.69G>A synonymous_variant 0.15
PPE35 2170547 c.66A>C synonymous_variant 0.13
PPE35 2170576 p.Ala13Thr missense_variant 0.2
Rv1979c 2221806 c.1359G>C synonymous_variant 0.25
Rv1979c 2222288 p.Ala293Thr missense_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222378 p.Val263Ile missense_variant 0.22
Rv1979c 2222538 c.627C>A synonymous_variant 0.2
Rv1979c 2222705 p.Phe154Ile missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289777 c.-536G>A upstream_gene_variant 0.13
pncA 2290129 c.-888C>A upstream_gene_variant 1.0
kasA 2518060 c.-55C>T upstream_gene_variant 0.22
kasA 2518132 c.18C>T synonymous_variant 0.89
kasA 2518146 c.36delC frameshift_variant 0.18
kasA 2518394 p.Leu94Ile missense_variant 0.17
kasA 2518798 c.684G>A synonymous_variant 0.15
kasA 2518924 c.810C>A synonymous_variant 0.25
kasA 2519035 c.921C>T synonymous_variant 1.0
kasA 2519098 c.984C>T synonymous_variant 0.13
eis 2714205 c.1128C>T synonymous_variant 0.25
eis 2714221 p.Ala371Asp missense_variant 0.22
eis 2714239 p.Arg365Leu missense_variant 0.2
eis 2714714 p.Ala207Ser missense_variant 0.25
eis 2714717 p.Ala206Thr missense_variant 0.2
eis 2714793 p.Glu180Asp missense_variant 0.29
eis 2715481 c.-149G>T upstream_gene_variant 0.4
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747052 p.Ala183Ser missense_variant 0.17
pepQ 2859938 p.Gly161Ser missense_variant 0.17
pepQ 2860023 c.396C>A synonymous_variant 0.17
pepQ 2860156 p.Gly88Val missense_variant 0.5
pepQ 2860615 c.-197T>C upstream_gene_variant 0.13
ribD 2987031 p.Pro65Ser missense_variant 0.18
ribD 2987279 c.441G>A synonymous_variant 0.22
ribD 2987454 p.Asp206Tyr missense_variant 0.2
ribD 2987509 p.Ala224Val missense_variant 0.14
Rv2752c 3064649 c.1543C>T synonymous_variant 0.12
Rv2752c 3064871 p.Ala441Ser missense_variant 0.22
Rv2752c 3065686 p.Gly169Val missense_variant 0.25
Rv2752c 3065769 c.423C>T synonymous_variant 0.15
thyX 3067604 c.342G>T synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087278 c.459A>G synonymous_variant 0.29
fbiD 3338997 c.-121C>A upstream_gene_variant 0.22
fbiD 3339332 p.Ala72Glu missense_variant 0.4
fbiD 3339417 c.300A>G synonymous_variant 1.0
fbiD 3339490 p.Leu125Phe missense_variant 0.15
Rv3083 3448548 c.45C>G synonymous_variant 0.15
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448729 p.Ala76Thr missense_variant 0.33
Rv3083 3448835 p.Ser111Ile missense_variant 1.0
Rv3083 3449616 p.Met371Ile missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474160 p.Gly52Trp missense_variant 0.2
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474963 c.957G>T synonymous_variant 0.22
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568440 p.Lys80Asn missense_variant 0.2
Rv3236c 3612386 p.Ala244Val missense_variant 0.15
Rv3236c 3612566 p.Gly184Val missense_variant 0.29
Rv3236c 3612931 c.186G>T synonymous_variant 0.12
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiB 3642073 p.Arg180His missense_variant 0.12
fbiB 3642086 c.552C>A synonymous_variant 0.12
fbiB 3642613 p.Tyr360Cys missense_variant 0.25
alr 3840311 c.1110C>T synonymous_variant 0.2
alr 3840440 c.981G>A synonymous_variant 0.13
alr 3840853 p.Leu190Met missense_variant 0.18
alr 3841181 c.240C>T synonymous_variant 0.17
ddn 3986993 c.150C>T synonymous_variant 0.2
ddn 3987198 p.Arg119Ser missense_variant 0.4
clpC1 4038702 p.Leu668Gln missense_variant 0.25
clpC1 4038781 p.Leu642Phe missense_variant 0.13
clpC1 4038813 p.His631Arg missense_variant 0.12
clpC1 4039556 c.1149G>T synonymous_variant 0.13
clpC1 4039915 p.Asp264Tyr missense_variant 0.17
clpC1 4040116 p.Ile197Phe missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044394 c.-113C>T upstream_gene_variant 0.2
embC 4240107 p.Leu82* stop_gained 0.25
embC 4240456 c.598delG frameshift_variant 0.11
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241159 p.Ala433Ser missense_variant 0.18
embC 4241177 p.Gly439Trp missense_variant 0.15
embC 4241777 p.Gly639Cys missense_variant 0.13
embC 4242350 p.Pro830Ser missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243427 c.195G>A synonymous_variant 0.12
embA 4243727 p.Glu165Asp missense_variant 0.4
embA 4243899 p.Ala223Thr missense_variant 0.14
embA 4244007 p.Ala259Thr missense_variant 0.25
embA 4244038 p.Ala269Asp missense_variant 0.25
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4244423 p.Glu397Asp missense_variant 0.15
embA 4245056 c.1824C>T synonymous_variant 0.18
embA 4245654 p.Asp808Tyr missense_variant 0.2
embA 4245800 p.Trp856* stop_gained 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246347 p.Thr1039Ala missense_variant 0.2
embA 4246365 p.Tyr1045His missense_variant 0.17
embA 4246460 p.Glu1076Asp missense_variant 0.14
embB 4246800 p.Gly96Val missense_variant 0.13
embB 4246825 p.Lys104Asn missense_variant 0.17
embB 4247482 p.Phe323Leu missense_variant 0.67
embB 4247628 p.Arg372Leu missense_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247839 c.1326G>A synonymous_variant 0.13
embB 4247875 c.1362G>T synonymous_variant 0.12
embB 4248231 p.Arg573Leu missense_variant 0.14
embB 4248358 c.1845C>T synonymous_variant 0.17
embB 4248515 p.Val668Ile missense_variant 1.0
embB 4248875 p.Phe788Leu missense_variant 0.12
embB 4249433 p.Leu974Met missense_variant 0.14
embB 4249649 c.3139delC frameshift_variant 0.22
aftB 4267002 p.Arg612Gln missense_variant 0.25
aftB 4267100 c.1737C>T synonymous_variant 0.15
aftB 4267147 p.Ala564Ser missense_variant 0.17
aftB 4267373 p.Phe488Leu missense_variant 0.15
aftB 4267435 p.Pro468Thr missense_variant 0.29
aftB 4268852 c.-16G>A upstream_gene_variant 0.14
aftB 4269018 c.-182G>T upstream_gene_variant 0.15
aftB 4269264 c.-428C>A upstream_gene_variant 0.5
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269515 p.Val107Met missense_variant 0.12
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4327360 c.-189C>G upstream_gene_variant 1.0
ethA 4327439 p.Ala12Val missense_variant 0.25
ethA 4327536 c.-63C>A upstream_gene_variant 0.25
ethA 4328201 c.-728G>A upstream_gene_variant 0.12
ethA 4328332 c.-859G>A upstream_gene_variant 0.5
ethA 4328439 c.-966C>A upstream_gene_variant 0.5
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407703 p.Ala167Val missense_variant 0.12
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407958 p.Ala82Glu missense_variant 0.2
gid 4407986 p.Gly73Trp missense_variant 0.17
gid 4408100 c.103C>T synonymous_variant 0.22
gid 4408101 c.102G>C synonymous_variant 0.18