TB-Profiler result

Run: ERR8665585
Summary

Run ID: ERR8665585

Sample name:

Date: 02-04-2023 07:32:54

Number of reads: 467035

Percentage reads mapped: 99.55

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289040 p.Trp68Gly missense_variant 0.89 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326087 c.1386delA frameshift_variant 1.0 ethionamide, 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 5511 p.Ser91Tyr missense_variant 0.25
gyrA 6652 c.-650C>A upstream_gene_variant 0.25
gyrA 6694 c.-608C>A upstream_gene_variant 0.33
gyrB 7215 p.Arg659Leu missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7404 p.Val35Met missense_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9350 p.Phe683Leu missense_variant 0.22
gyrA 9416 p.Phe705Leu missense_variant 0.18
gyrA 9807 p.Thr836Ser missense_variant 0.33
fgd1 491453 p.Gly224Val missense_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575961 p.Gln205Arg missense_variant 0.18
ccsA 620202 c.312G>T synonymous_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620640 p.Trp250Cys missense_variant 0.22
rpoB 760079 p.Glu91Asp missense_variant 0.14
rpoB 760265 p.Met153Ile missense_variant 0.18
rpoC 762947 c.-423C>A upstream_gene_variant 0.27
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765323 p.Gly652Cys missense_variant 0.17
rpoC 766676 p.Asp1103Tyr missense_variant 0.21
rpoC 767255 p.Asp1296Tyr missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776158 p.Asp775Tyr missense_variant 0.27
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777461 c.1020G>T synonymous_variant 0.33
mmpL5 778153 p.Asp110Tyr missense_variant 0.29
mmpL5 778777 c.-297C>A upstream_gene_variant 0.17
mmpS5 779496 c.-591G>T upstream_gene_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303378 p.Arg150Ser missense_variant 0.18
fbiC 1303710 p.Leu260Phe missense_variant 0.18
fbiC 1304014 p.Pro362Ser missense_variant 0.33
fbiC 1304559 p.Glu543Asp missense_variant 0.25
fbiC 1305432 c.2502C>A synonymous_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416672 p.Gly226Cys missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476322 n.2665C>G non_coding_transcript_exon_variant 0.13
rrl 1476403 n.2746G>T non_coding_transcript_exon_variant 0.17
fabG1 1673587 p.Gly50* stop_gained 0.67
fabG1 1673911 p.Ala158Thr missense_variant 0.2
rpsA 1833402 c.-140G>T upstream_gene_variant 0.25
rpsA 1834141 c.600C>T synonymous_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834180 p.Lys213Asn missense_variant 0.15
rpsA 1834579 c.1038C>A synonymous_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918089 c.150C>A synonymous_variant 0.67
ndh 2102040 p.Gly335Cys missense_variant 0.33
ndh 2102640 p.Ala135Ser missense_variant 0.2
katG 2154346 p.Pro589His missense_variant 0.17
katG 2154645 c.1467C>T synonymous_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154884 p.Lys410* stop_gained 0.2
katG 2156517 c.-406C>A upstream_gene_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168306 p.Phe769Leu missense_variant 0.25
PPE35 2169422 c.1191G>T synonymous_variant 0.18
PPE35 2170389 p.Trp75Leu missense_variant 0.15
Rv1979c 2222421 c.744G>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289152 c.90C>A synonymous_variant 0.25
kasA 2518275 p.Trp54Leu missense_variant 0.17
kasA 2519178 p.Ser355* stop_gained 0.25
kasA 2519316 p.Ser401* stop_gained 0.29
eis 2714192 p.Gln381Lys missense_variant 0.17
eis 2714795 p.Glu180* stop_gained 0.25
eis 2714917 p.Glu139Gly missense_variant 0.22
eis 2715055 p.Arg93Gln missense_variant 0.2
ahpC 2726122 c.-71T>C upstream_gene_variant 0.11
ahpC 2726484 p.Ala98Ser missense_variant 0.13
folC 2746149 p.Arg484Ser missense_variant 0.25
folC 2746279 c.1320C>T synonymous_variant 0.2
folC 2746499 p.Ala367Val missense_variant 0.14
pepQ 2859558 c.861C>T synonymous_variant 0.18
Rv2752c 3066159 c.33G>T synonymous_variant 0.25
Rv2752c 3067178 c.-987G>T upstream_gene_variant 0.29
thyX 3067349 c.597G>T synonymous_variant 0.33
thyX 3068073 c.-128C>A upstream_gene_variant 0.15
thyA 3073687 p.Ala262Val missense_variant 0.2
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087600 p.Gly261Cys missense_variant 0.14
ald 3087928 p.Leu370Pro missense_variant 0.18
Rv3083 3448344 c.-160G>T upstream_gene_variant 0.22
Rv3083 3449033 p.Gly177Val missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474123 c.117G>T synonymous_variant 0.2
fprA 3474652 p.Ala216Ser missense_variant 0.25
fprA 3475074 c.1068C>A synonymous_variant 0.2
whiB7 3568795 c.-116A>G upstream_gene_variant 1.0
Rv3236c 3612395 p.Ala241Val missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613149 c.-33G>T upstream_gene_variant 0.22
fbiB 3641695 p.Ser54Tyr missense_variant 0.15
fbiB 3642774 p.Leu414Met missense_variant 0.2
rpoA 3877851 p.Phe219Leu missense_variant 0.29
rpoA 3878056 p.Gln151Arg missense_variant 0.13
ddn 3986652 c.-192C>T upstream_gene_variant 0.22
ddn 3986673 c.-171C>A upstream_gene_variant 0.22
clpC1 4040390 c.315C>A synonymous_variant 0.33
embC 4239795 c.-68C>G upstream_gene_variant 0.13
embC 4240140 p.Gly93Val missense_variant 0.2
embC 4240298 p.Gln146Lys missense_variant 0.21
embC 4240443 p.Arg194His missense_variant 0.18
embC 4240668 p.Ser269* stop_gained 0.25
embC 4241914 c.2052C>T synonymous_variant 0.4
embC 4242527 p.Gly889Arg missense_variant 0.22
embA 4242637 c.-596C>A upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242840 p.Cys993Phe missense_variant 0.14
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243429 p.Ala66Val missense_variant 0.17
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243813 p.Arg194Leu missense_variant 0.17
embA 4243953 p.Arg241Ser missense_variant 0.22
embA 4244379 p.Pro383Thr missense_variant 0.29
embA 4245326 c.2094C>A synonymous_variant 0.22
embB 4247274 p.Arg254Met missense_variant 0.15
embB 4248667 p.Phe718Leu missense_variant 0.17
embB 4249081 p.Ser856Arg missense_variant 0.13
embB 4249166 p.Gly885Arg missense_variant 0.17
aftB 4267383 p.Ala485Glu missense_variant 0.2
aftB 4267428 p.Ser470* stop_gained 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267955 c.882G>T synonymous_variant 0.22
aftB 4268156 p.Phe227Leu missense_variant 0.13
ubiA 4269100 p.Gly245Val missense_variant 0.18
ethA 4327603 c.-130G>T upstream_gene_variant 0.2
ethR 4327856 p.Trp103Leu missense_variant 0.2
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408194 c.9G>T synonymous_variant 0.18