TB-Profiler result

Run: ERR6336764
Summary

Run ID: ERR6336764

Sample name:

Date: 02-04-2023 02:02:23

Number of reads: 738157

Percentage reads mapped: 99.05

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 5534 p.Val99Met missense_variant 0.67
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6631 c.-671C>T upstream_gene_variant 0.15
gyrA 7346 c.45C>T synonymous_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9079 p.Gly593Glu missense_variant 0.2
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491041 p.Ala87Thr missense_variant 0.2
fgd1 491229 c.447C>T synonymous_variant 0.13
fgd1 491451 p.Asp223Glu missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 576136 c.789T>C synonymous_variant 0.22
ccsA 620063 p.Ser58Asn missense_variant 0.17
rpoB 759925 p.Glu40Gly missense_variant 0.17
rpoB 759934 p.Glu43Gly missense_variant 0.29
rpoB 760029 p.Asn75Asp missense_variant 0.15
rpoB 760867 p.Gly354Asp missense_variant 0.18
rpoB 761152 p.Leu449Gln missense_variant 0.33
rpoB 761558 c.1752C>T synonymous_variant 0.17
rpoB 761742 p.Glu646Lys missense_variant 0.17
rpoB 762203 c.2397G>A synonymous_variant 0.22
rpoB 762864 p.Gly1020Ser missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763773 p.Val135Glu missense_variant 0.15
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764734 p.Phe455Leu missense_variant 0.13
rpoC 764964 p.Phe532Ser missense_variant 0.11
rpoC 765323 p.Gly652Ser missense_variant 0.2
rpoC 765685 c.2316G>A synonymous_variant 0.17
rpoC 766289 p.Val974Met missense_variant 0.29
rpoC 766736 p.Arg1123Trp missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777773 p.Val236Gly missense_variant 0.15
mmpS5 778614 p.Ser98Thr missense_variant 0.15
mmpL5 778894 c.-414T>C upstream_gene_variant 0.11
mmpL5 779166 c.-686C>T upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781702 p.Ala48Gly missense_variant 0.15
rplC 801161 p.Ser118Phe missense_variant 0.12
rplC 801275 p.Thr156Met missense_variant 0.4
fbiC 1303326 c.396C>T synonymous_variant 0.14
fbiC 1303815 c.885C>T synonymous_variant 0.12
fbiC 1304827 p.Phe633Leu missense_variant 0.29
fbiC 1305147 c.2217C>T synonymous_variant 0.12
Rv1258c 1406169 p.Gly391Val missense_variant 0.29
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406502 p.Val280Ala missense_variant 0.12
Rv1258c 1406529 p.Gly271Ala missense_variant 0.18
Rv1258c 1407157 p.Ala62Thr missense_variant 0.2
embR 1416445 c.903C>T synonymous_variant 0.4
embR 1416962 p.Gly129Asp missense_variant 0.5
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417077 p.Arg91Trp missense_variant 0.25
embR 1417087 c.261G>T synonymous_variant 0.17
embR 1417094 p.Gly85Ala missense_variant 0.2
embR 1417489 c.-142G>C upstream_gene_variant 0.17
embR 1417500 c.-153C>T upstream_gene_variant 0.13
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473086 n.1241C>T non_coding_transcript_exon_variant 0.17
rrs 1473137 n.1292G>A non_coding_transcript_exon_variant 0.13
rrl 1474515 n.858G>A non_coding_transcript_exon_variant 0.15
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
rrl 1475004 n.1347C>T non_coding_transcript_exon_variant 0.29
rrl 1476562 n.2908dupG non_coding_transcript_exon_variant 0.13
fabG1 1673317 c.-123T>C upstream_gene_variant 0.11
fabG1 1673549 p.Ala37Val missense_variant 0.4
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674187 c.-15A>G upstream_gene_variant 0.1
inhA 1674935 p.Leu245Arg missense_variant 0.2
rpsA 1834929 p.Ser463Leu missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918535 p.His199Arg missense_variant 0.11
ndh 2101974 p.Ala357Thr missense_variant 0.12
ndh 2101985 p.Gly353Asp missense_variant 0.13
ndh 2102258 p.Ser262Phe missense_variant 0.25
ndh 2102754 p.Gln97Glu missense_variant 0.25
katG 2154602 p.Gly504Arg missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155394 p.Asp240Asn missense_variant 0.22
katG 2156300 c.-189G>A upstream_gene_variant 0.15
katG 2156367 c.-256G>A upstream_gene_variant 0.25
PPE35 2167660 p.Thr985Ala missense_variant 0.13
PPE35 2167772 c.2841C>G synonymous_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169123 p.Thr497Ile missense_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222783 p.Ala128Thr missense_variant 0.2
Rv1979c 2222870 p.Ala99Thr missense_variant 0.13
Rv1979c 2223269 c.-105G>A upstream_gene_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289323 c.-82G>A upstream_gene_variant 0.12
pncA 2289534 c.-293G>C upstream_gene_variant 0.14
pncA 2289539 c.-298C>T upstream_gene_variant 0.14
kasA 2517963 c.-152G>A upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
kasA 2519215 c.1101C>T synonymous_variant 0.5
kasA 2519279 c.1169_1170delGC frameshift_variant 0.25
eis 2715150 p.Met61Ile missense_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726678 c.486G>A synonymous_variant 0.33
ahpC 2726746 p.Leu185Arg missense_variant 0.25
folC 2747044 c.555C>T synonymous_variant 0.13
ribD 2987032 p.Pro65Leu missense_variant 0.14
Rv2752c 3064822 p.Val457Ala missense_variant 0.22
Rv2752c 3064825 p.Asp456Val missense_variant 0.22
Rv2752c 3064828 p.Gly455Asp missense_variant 0.25
thyX 3067594 p.Val118Leu missense_variant 0.12
thyA 3073903 p.Ala190Val missense_variant 0.2
thyA 3074046 c.426G>A synonymous_variant 0.17
thyA 3074065 p.Gly136Asp missense_variant 0.14
thyA 3074441 p.Val11Met missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086925 p.Gln36* stop_gained 0.18
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448669 p.Asp56Asn missense_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448944 c.441G>C synonymous_variant 0.14
Rv3083 3449140 p.Ser213Ala missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474076 p.Lys24Glu missense_variant 0.15
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
Rv3236c 3612548 p.Ala190Val missense_variant 0.12
Rv3236c 3612701 c.415delG frameshift_variant 0.25
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640687 p.Asp49Asn missense_variant 0.22
fbiB 3641253 c.-282C>T upstream_gene_variant 0.18
fbiB 3641849 c.316delG frameshift_variant 0.12
fbiB 3642653 c.1119C>T synonymous_variant 0.14
fbiB 3642671 c.1137G>A synonymous_variant 0.17
alr 3841471 c.-51A>G upstream_gene_variant 0.17
rpoA 3877586 c.921delA frameshift_variant 0.22
rpoA 3877646 p.Asn288Tyr missense_variant 0.18
rpoA 3877696 p.Thr271Ser missense_variant 0.12
rpoA 3877897 p.Pro204Leu missense_variant 0.13
rpoA 3878484 c.24C>T synonymous_variant 0.13
rpoA 3878668 c.-161C>T upstream_gene_variant 0.4
clpC1 4039254 p.Ile484Thr missense_variant 0.22
clpC1 4039828 p.Val293Ile missense_variant 0.12
clpC1 4040081 c.624C>T synonymous_variant 0.2
clpC1 4040146 c.559C>T synonymous_variant 0.2
clpC1 4040170 p.Thr179Ala missense_variant 0.2
clpC1 4040254 p.Ala151Ser missense_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044110 p.Tyr58Asp missense_variant 0.14
embC 4239989 c.127C>T synonymous_variant 0.25
embC 4240172 p.Val104Met missense_variant 0.14
embC 4240411 c.549G>C synonymous_variant 0.67
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241287 c.1425G>A synonymous_variant 0.2
embC 4241387 p.Ser509Gly missense_variant 0.11
embC 4241474 c.1612C>T synonymous_variant 0.25
embA 4242268 c.-965T>C upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4244883 c.1652dupG frameshift_variant 0.2
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247334 p.Arg274His missense_variant 0.22
embB 4247354 p.Ala281Thr missense_variant 0.22
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247592 p.Val360Ala missense_variant 0.11
embB 4247593 c.1081delT frameshift_variant 0.11
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248637 c.2124G>A synonymous_variant 0.4
embB 4248810 p.Pro766Leu missense_variant 0.29
embB 4249487 p.Leu992Val missense_variant 0.14
embB 4249719 p.Thr1069Ile missense_variant 0.13
aftB 4267032 p.Ile602Thr missense_variant 0.13
aftB 4268760 p.Trp26* stop_gained 0.2
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269393 c.-557G>A upstream_gene_variant 0.13
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ubiA 4270011 c.-178A>G upstream_gene_variant 0.14
ubiA 4270016 c.-183G>A upstream_gene_variant 0.22
ubiA 4270021 c.-188T>C upstream_gene_variant 0.2
ethA 4327014 p.Ser154Ala missense_variant 0.11
ethA 4327479 c.-6G>A upstream_gene_variant 0.18
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 4407791 p.Ala138Thr missense_variant 0.22
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407933 c.270C>T synonymous_variant 0.22
gid 4408412 c.-210G>A upstream_gene_variant 0.33