TB-Profiler result

Run: ERR6336712
Summary

Run ID: ERR6336712

Sample name:

Date: 02-04-2023 02:00:16

Number of reads: 667680

Percentage reads mapped: 98.81

Strain: lineage1.2.1.2.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 Indo-Oceanic NA RD239 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 5327 p.Pro30Ser missense_variant 0.12
gyrB 6057 p.Ser273Thr missense_variant 0.12
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6930 p.Ala564Val missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7473 p.Ala58Thr missense_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8287 c.987delT frameshift_variant 0.14
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9239 c.1938C>T synonymous_variant 1.0
gyrA 9249 p.Ala650Thr missense_variant 0.12
gyrA 9255 p.Asn652Asp missense_variant 0.12
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9591 p.Gly764Arg missense_variant 0.14
fgd1 490724 c.-59G>A upstream_gene_variant 0.22
fgd1 491081 p.Arg100Leu missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491761 p.Asp327Asn missense_variant 0.12
mshA 575307 c.-41G>A upstream_gene_variant 0.2
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575809 c.462C>T synonymous_variant 0.12
mshA 576164 p.Arg273Cys missense_variant 0.33
mshA 576217 c.873delC frameshift_variant 0.25
mshA 576456 p.Val370Gly missense_variant 0.2
rpoB 760867 p.Gly354Asp missense_variant 0.22
rpoB 760999 p.Met398Thr missense_variant 0.4
rpoB 761844 p.Gln680* stop_gained 0.14
rpoB 762198 p.Gly798Ser missense_variant 0.12
rpoB 762409 p.Ala868Asp missense_variant 0.13
rpoC 762524 c.-846G>A upstream_gene_variant 0.18
rpoC 762875 c.-495C>T upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763198 p.Val1131Ala missense_variant 0.12
rpoC 763444 c.75T>C synonymous_variant 0.14
rpoC 763470 p.Ile34Thr missense_variant 0.13
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764117 p.Glu250* stop_gained 0.29
rpoC 765111 c.1744delG frameshift_variant 0.15
rpoC 766110 p.Pro914Leu missense_variant 0.25
rpoC 766147 c.2778C>G synonymous_variant 0.29
rpoC 766463 p.Gln1032Glu missense_variant 0.4
rpoC 766701 p.Leu1111Pro missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775732 p.Asp917His missense_variant 0.13
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776225 p.Glu752Asp missense_variant 0.12
mmpL5 776243 c.2238C>T synonymous_variant 0.14
mmpL5 776430 p.Arg684His missense_variant 0.2
mmpL5 776503 p.Glu660Lys missense_variant 0.17
mmpL5 777071 c.1410G>A synonymous_variant 0.25
mmpL5 778311 p.Gly57Ala missense_variant 0.12
mmpL5 778483 c.-3C>T upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781660 p.Cys34Tyr missense_variant 0.15
rplC 800772 c.-37G>C upstream_gene_variant 0.14
rplC 800986 p.Arg60Cys missense_variant 0.17
fbiC 1304503 p.Leu525Met missense_variant 0.17
fbiC 1304596 p.Asn556Asp missense_variant 0.17
fbiC 1304689 p.Arg587Trp missense_variant 0.18
Rv1258c 1406141 c.1200G>A synonymous_variant 0.12
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406697 p.Gly215Glu missense_variant 0.18
embR 1416259 c.1089G>C synonymous_variant 0.17
embR 1416262 c.1086G>C synonymous_variant 0.14
embR 1416388 c.959delT frameshift_variant 0.17
embR 1416480 p.Ala290Pro missense_variant 0.25
embR 1416639 p.Asp237Asn missense_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417134 p.Ile72Val missense_variant 0.33
embR 1417280 p.Ile23Thr missense_variant 0.12
embR 1417371 c.-24A>T upstream_gene_variant 0.2
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
atpE 1461219 c.175T>C synonymous_variant 0.1
atpE 1461251 c.207G>C synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473024 n.1179G>C non_coding_transcript_exon_variant 0.5
rrl 1473694 n.37C>T non_coding_transcript_exon_variant 0.4
rrl 1474170 n.513G>T non_coding_transcript_exon_variant 0.67
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
rrl 1476244 n.2587G>A non_coding_transcript_exon_variant 0.22
inhA 1674057 c.-145C>T upstream_gene_variant 0.22
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
rpsA 1833920 p.Lys127Glu missense_variant 0.12
rpsA 1834015 c.474G>A synonymous_variant 0.13
rpsA 1834260 p.Leu240Pro missense_variant 0.11
rpsA 1834267 p.Lys243Arg missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918664 p.Trp242Leu missense_variant 0.4
ndh 2102165 p.Ser293Leu missense_variant 0.25
ndh 2102237 p.Ile269Asn missense_variant 0.18
ndh 2102685 p.Gly120Cys missense_variant 0.15
ndh 2102957 p.Ala29Val missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169690 p.Gly308Val missense_variant 0.15
PPE35 2169695 p.Gln306His missense_variant 0.15
Rv1979c 2222082 c.1083C>T synonymous_variant 0.12
Rv1979c 2222085 c.1080G>T synonymous_variant 0.12
Rv1979c 2222302 p.Thr288Ile missense_variant 0.22
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222492 p.Thr225Ala missense_variant 0.25
Rv1979c 2222503 p.Met221Lys missense_variant 0.22
Rv1979c 2222654 p.Ala171Thr missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288681 c.561A>G stop_lost&splice_region_variant 0.29
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519162 p.Val350Ile missense_variant 0.2
eis 2714819 p.Arg172Cys missense_variant 0.15
eis 2714988 c.345C>T synonymous_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726311 p.Ser40Asn missense_variant 0.18
ahpC 2726428 p.Asp79Ala missense_variant 0.15
folC 2746322 p.Gly426Ala missense_variant 0.2
folC 2746325 p.Phe425Cys missense_variant 0.18
folC 2746641 p.Gln320* stop_gained 0.18
folC 2746890 c.707_708delGT frameshift_variant 0.2
folC 2747524 c.75G>A synonymous_variant 0.22
Rv2752c 3064548 c.1644G>A synonymous_variant 0.12
Rv2752c 3064553 p.Arg547Cys missense_variant 0.12
Rv2752c 3064866 c.1326G>A synonymous_variant 0.25
Rv2752c 3065301 c.891C>T synonymous_variant 0.2
Rv2752c 3066152 p.Gly14Ser missense_variant 0.22
thyX 3067222 p.Ala242Pro missense_variant 0.29
thyX 3067726 p.Glu74Lys missense_variant 0.13
thyX 3067882 p.Asp22Asn missense_variant 0.15
thyX 3068039 c.-94C>G upstream_gene_variant 0.15
thyA 3074357 p.Ser39Ala missense_variant 0.25
thyA 3074385 c.87G>C synonymous_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087618 p.Ile267Val missense_variant 0.1
ald 3087740 c.921G>A synonymous_variant 0.15
fbiD 3339417 c.300A>G synonymous_variant 1.0
fbiD 3339488 p.Glu124Ala missense_variant 0.11
Rv3083 3448522 p.Val7Leu missense_variant 0.11
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448720 p.Lys73Glu missense_variant 0.17
Rv3083 3449183 p.Ser227Phe missense_variant 0.5
Rv3083 3449280 c.777G>A synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474002 c.-5C>A upstream_gene_variant 0.14
fprA 3474426 c.420G>A synonymous_variant 0.25
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
whiB7 3568572 c.108C>T synonymous_variant 0.15
whiB7 3568646 c.33dupC frameshift_variant 0.18
Rv3236c 3612094 c.1023C>T synonymous_variant 0.17
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640652 p.Ala37Val missense_variant 0.29
fbiA 3640679 p.Asn46Ile missense_variant 0.33
fbiA 3640841 p.Asp100Val missense_variant 0.15
fbiB 3641529 c.-6G>A upstream_gene_variant 0.2
fbiB 3642868 p.Leu445Pro missense_variant 0.13
alr 3840212 c.1209C>T synonymous_variant 0.14
alr 3840270 p.Gly384Ala missense_variant 0.22
alr 3840834 p.His196Leu missense_variant 0.17
rpoA 3877492 c.1015delC frameshift_variant 0.17
rpoA 3877591 p.Leu306Ala missense_variant 0.13
rpoA 3877639 p.Gly290Val missense_variant 0.15
rpoA 3877866 c.642G>C synonymous_variant 0.13
ddn 3986794 c.-50G>C upstream_gene_variant 0.17
clpC1 4038398 c.2307G>A synonymous_variant 0.15
clpC1 4038740 c.1965G>C synonymous_variant 0.12
clpC1 4038752 p.Gln651His missense_variant 0.13
clpC1 4039924 p.Tyr261His missense_variant 0.12
clpC1 4039929 p.Ser259Thr missense_variant 0.12
clpC1 4039932 p.Gly258Ala missense_variant 0.12
clpC1 4040032 p.Val225Ile missense_variant 0.14
clpC1 4040057 c.648C>T synonymous_variant 0.14
clpC1 4040087 c.618G>A synonymous_variant 0.18
clpC1 4040219 c.486C>T synonymous_variant 0.15
clpC1 4040356 p.Glu117Lys missense_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044319 c.-38G>A upstream_gene_variant 0.15
embC 4239677 c.-186C>T upstream_gene_variant 0.14
embC 4239735 c.-128C>A upstream_gene_variant 0.2
embC 4240661 c.801delG frameshift_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242368 p.Arg836Gly missense_variant 0.17
embC 4242416 p.Gly852Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242904 p.Asp1014Glu missense_variant 0.22
embA 4242964 c.-269C>T upstream_gene_variant 0.25
embA 4243272 p.Arg14Cys missense_variant 0.13
embA 4243291 p.Ser20Leu missense_variant 0.13
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243703 c.471C>T synonymous_variant 0.15
embA 4244343 p.Ala371Thr missense_variant 0.13
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245194 c.1962G>A synonymous_variant 0.12
embA 4245651 p.Thr807Ala missense_variant 0.17
embA 4245660 p.Ala810Thr missense_variant 0.14
embA 4245772 p.Asn847Ile missense_variant 0.14
embA 4245782 c.2551delA frameshift_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246567 c.54_55insT frameshift_variant 0.4
embB 4247041 c.528C>T synonymous_variant 1.0
embB 4247105 p.Pro198Ser missense_variant 0.2
embB 4247109 p.Gly199Glu missense_variant 0.2
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247875 c.1362G>T synonymous_variant 0.14
embB 4248683 p.Ala724Ser missense_variant 0.13
embB 4248694 c.2181G>A synonymous_variant 0.13
embB 4248699 p.Gln729Pro missense_variant 0.13
embB 4248773 p.Leu754Phe missense_variant 0.13
aftB 4267085 c.1752G>A synonymous_variant 0.15
aftB 4267695 p.Gly381Glu missense_variant 0.24
aftB 4268108 c.729G>A synonymous_variant 0.25
aftB 4268444 c.393C>T synonymous_variant 0.4
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269468 c.365delC frameshift_variant 0.15
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ethA 4326228 p.Thr416Ala missense_variant 0.15
ethA 4326350 p.Ser375Tyr missense_variant 0.12
ethA 4327389 p.Thr29Ala missense_variant 0.18
ethA 4327419 p.Ala19Pro missense_variant 0.15
ethA 4328291 c.-818C>T upstream_gene_variant 0.13
whiB6 4338289 p.Gly78Glu missense_variant 0.15
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 4407535 p.Thr223Met missense_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408107 p.Glu32Asp missense_variant 0.25