TB-Profiler result

Run: ERR6336752
Summary

Run ID: ERR6336752

Sample name:

Date: 02-04-2023 02:02:09

Number of reads: 1282011

Percentage reads mapped: 98.78

Strain: lineage1.2.1.2

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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
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 2155786 p.Ala109Val missense_variant 0.2 isoniazid
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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7445 c.144C>T synonymous_variant 0.25
gyrA 7446 p.Lys49Glu missense_variant 0.25
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7635 p.Gly112Ser missense_variant 0.2
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9071 c.1770_1771insC frameshift_variant 0.12
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9189 p.Gly630Arg missense_variant 0.11
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9293 c.1992G>A synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490715 c.-68A>G upstream_gene_variant 0.14
fgd1 490872 c.90C>T synonymous_variant 0.14
fgd1 491152 p.Glu124Lys missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575194 c.-153delC upstream_gene_variant 0.13
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575398 c.51T>C synonymous_variant 0.4
mshA 575418 p.Ala24Gly missense_variant 0.29
mshA 575752 c.405G>A synonymous_variant 0.12
mshA 576160 c.813C>T synonymous_variant 0.29
mshA 576502 c.1155C>T synonymous_variant 0.5
mshA 576774 p.Arg476His missense_variant 0.12
ccsA 620123 p.Arg78Leu missense_variant 0.33
ccsA 620743 p.Ala285Pro missense_variant 0.14
rpoB 761647 p.Arg614His missense_variant 0.22
rpoB 761701 p.Ala632Val missense_variant 0.29
rpoB 761710 p.Val635Asp missense_variant 0.33
rpoB 761713 p.Val636Asp missense_variant 0.36
rpoB 762131 c.2325C>T synonymous_variant 0.13
rpoB 762208 p.Thr801Ile missense_variant 0.22
rpoB 762223 p.Thr806Ile missense_variant 0.14
rpoB 762945 p.Thr1047Ala missense_variant 0.25
rpoB 762952 p.Gln1049Arg missense_variant 0.19
rpoB 762955 p.Pro1050Leu missense_variant 0.19
rpoC 762962 c.-408C>T upstream_gene_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763610 p.Glu81Lys missense_variant 0.12
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 763965 p.Asp199Val missense_variant 1.0
rpoC 764710 p.Met447Ile missense_variant 1.0
rpoC 765532 c.2163C>T synonymous_variant 0.18
rpoC 766074 p.Ala902Gly missense_variant 0.18
rpoC 766102 c.2733C>T synonymous_variant 0.29
rpoC 766658 p.Arg1097Trp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778594 c.-114C>T upstream_gene_variant 0.25
mmpR5 779279 p.Pro97Leu missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304082 c.1152C>T synonymous_variant 1.0
fbiC 1304503 c.1573C>T synonymous_variant 0.17
fbiC 1305251 p.Arg774Leu missense_variant 0.15
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406538 p.Ala268Gly missense_variant 0.29
Rv1258c 1406952 p.Glu130Thr missense_variant 0.2
Rv1258c 1407437 c.-97A>G upstream_gene_variant 0.13
embR 1416517 c.831C>T synonymous_variant 0.18
embR 1416960 p.Arg130Trp missense_variant 0.18
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
inhA 1673643 c.-559C>T upstream_gene_variant 0.12
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674690 c.489C>G synonymous_variant 0.12
inhA 1674769 p.Ala190Thr missense_variant 0.13
rpsA 1833387 c.-155G>A upstream_gene_variant 0.15
rpsA 1833975 p.Arg145His missense_variant 0.12
rpsA 1834922 p.Gly461Ser missense_variant 0.2
tlyA 1917834 c.-106A>G upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918177 p.Ala80Thr missense_variant 0.4
ndh 2102149 c.894C>T synonymous_variant 0.25
ndh 2102257 c.786C>T synonymous_variant 0.4
ndh 2102449 c.594G>A synonymous_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155304 p.His270Tyr missense_variant 0.17
katG 2155744 p.Gly123Ala missense_variant 1.0
katG 2156362 c.-251C>T upstream_gene_variant 0.15
katG 2156365 c.-254C>T upstream_gene_variant 0.15
katG 2156408 c.-297C>T upstream_gene_variant 0.18
katG 2156422 c.-311C>T upstream_gene_variant 0.17
katG 2156427 c.-316G>A upstream_gene_variant 0.17
katG 2156435 c.-324G>A upstream_gene_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170322 c.291C>T synonymous_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288708 c.534C>T synonymous_variant 0.2
pncA 2288774 c.468G>C synonymous_variant 0.11
pncA 2289216 p.Val9Thr missense_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518581 p.Leu156Pro missense_variant 0.22
kasA 2519048 p.Gly312Ser missense_variant 1.0
eis 2714344 p.Ala330Val missense_variant 0.25
eis 2714777 p.Val186Leu missense_variant 0.2
eis 2714864 p.Gly157Ser missense_variant 0.33
ahpC 2726002 c.-191G>A upstream_gene_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746201 c.1398C>T synonymous_variant 0.15
folC 2747531 p.Glu23Ala missense_variant 0.11
ribD 2987437 p.Gly200Glu missense_variant 0.14
ribD 2987532 p.Gly232Trp missense_variant 0.13
Rv2752c 3064668 c.1524G>A synonymous_variant 0.14
Rv2752c 3064988 p.Met402Val missense_variant 0.11
Rv2752c 3065002 p.His397Arg missense_variant 0.18
Rv2752c 3065026 p.Arg389Gln missense_variant 0.15
Rv2752c 3065551 p.Ser214Leu missense_variant 0.14
Rv2752c 3066209 c.-18C>T upstream_gene_variant 0.13
thyX 3067330 p.Val206Met missense_variant 0.2
thyX 3067997 c.-52T>C upstream_gene_variant 0.25
thyX 3068026 c.-81G>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086957 c.138C>T synonymous_variant 0.15
ald 3087230 c.411C>G synonymous_variant 0.22
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449354 p.Ser284Ile missense_variant 0.12
fprA 3473965 c.-42A>G upstream_gene_variant 0.13
fprA 3473984 c.-23G>A upstream_gene_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474698 p.Asp231Gly missense_variant 0.11
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568478 p.Gly68Ser missense_variant 0.2
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612368 p.Thr250Met missense_variant 0.2
Rv3236c 3612418 c.699C>T synonymous_variant 0.17
Rv3236c 3612599 p.Ala173Val missense_variant 0.4
Rv3236c 3612619 c.498G>A synonymous_variant 0.18
Rv3236c 3613267 c.-151G>A upstream_gene_variant 0.14
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiB 3641184 c.-351T>C upstream_gene_variant 0.17
fbiA 3641368 p.Tyr276His missense_variant 0.33
fbiB 3641418 c.-117C>T upstream_gene_variant 0.2
fbiA 3641438 p.Asp299Gly missense_variant 0.25
fbiB 3641866 p.Ser111Phe missense_variant 0.22
fbiB 3642210 p.Gly226Ser missense_variant 0.67
alr 3841171 p.Ala84Thr missense_variant 1.0
alr 3841253 c.168C>T synonymous_variant 0.2
rpoA 3877848 c.660C>T synonymous_variant 0.14
rpoA 3878567 c.-60C>G upstream_gene_variant 0.5
ddn 3987045 p.Arg68Cys missense_variant 0.2
clpC1 4038233 c.2472C>T synonymous_variant 0.33
clpC1 4039603 p.Ala368Pro missense_variant 0.15
clpC1 4040185 p.Phe174Leu missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040898 c.-194C>T upstream_gene_variant 0.12
embC 4239992 p.Ala44Thr missense_variant 0.13
embC 4240492 c.630G>A synonymous_variant 0.17
embC 4240553 p.Met231Val missense_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241290 c.1428C>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242808 c.-425C>T upstream_gene_variant 0.12
embA 4243372 p.Gln47Arg missense_variant 0.11
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243679 c.447C>T synonymous_variant 0.15
embA 4243681 p.Ala150Asp missense_variant 0.15
embA 4243736 c.505delC frameshift_variant 0.15
embA 4243744 p.Gly171Asp missense_variant 0.13
embA 4244398 p.Val389Gly missense_variant 0.2
embA 4244403 p.Val391Ile missense_variant 0.2
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.4
embB 4246548 p.Pro12Gln missense_variant 0.44
embB 4246555 c.42G>C synonymous_variant 0.39
embB 4246556 p.Ala15Pro missense_variant 0.39
embB 4246563 p.Leu17Trp missense_variant 0.35
embB 4246567 c.54G>T synonymous_variant 0.32
embB 4246613 p.Gly34Arg missense_variant 0.2
embB 4247559 p.Trp349Leu missense_variant 0.13
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4249347 p.Ala945Val missense_variant 0.33
embB 4249359 p.Val949Glu missense_variant 0.25
aftB 4267718 c.1119C>T synonymous_variant 0.33
aftB 4267759 p.Gly360Ser missense_variant 0.14
aftB 4267872 p.Gln322Leu missense_variant 0.25
aftB 4268218 p.Trp207Gly missense_variant 0.18
aftB 4268257 p.Gly194Arg missense_variant 0.22
aftB 4268441 c.396C>T synonymous_variant 0.12
aftB 4268516 c.321A>G synonymous_variant 0.11
aftB 4268869 c.-34delG upstream_gene_variant 0.22
aftB 4268894 c.-58G>A upstream_gene_variant 0.18
aftB 4268897 c.-61G>A upstream_gene_variant 0.17
ubiA 4269387 p.Glu149Asp missense_variant 1.0
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 0.18
ubiA 4270016 c.-183G>A upstream_gene_variant 0.18
ubiA 4270021 c.-188T>C upstream_gene_variant 0.22
ubiA 4270026 c.-193C>T upstream_gene_variant 0.22
ethA 4326903 p.Val191Met missense_variant 0.2
whiB6 4338349 p.Arg58His missense_variant 0.2
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 4407873 c.330G>T synonymous_variant 1.0
gid 4408068 p.Trp45Cys missense_variant 0.12
gid 4408316 c.-114C>T upstream_gene_variant 0.12