TB-Profiler result

Run: ERR8665589

Summary

Run ID: ERR8665589

Sample name:

Date: 02-04-2023 07:32:56

Number of reads: 493433

Percentage reads mapped: 99.57

Strain: lineage2.2

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
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
tlyA 1918517 c.582delC frameshift_variant 1.0 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288756 c.484_485dupGG frameshift_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg 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 6539 p.Asp434Asn missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9189 p.Gly630Trp missense_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9309 p.Asp670Tyr missense_variant 0.5
fgd1 490941 p.Phe53Leu missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575474 p.Asp43Tyr missense_variant 0.22
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576291 p.Leu315Pro missense_variant 0.22
ccsA 619795 c.-96C>T upstream_gene_variant 0.4
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620661 c.771C>A synonymous_variant 0.2
rpoB 760777 p.Ser324* stop_gained 0.25
rpoB 761561 c.1755C>A synonymous_variant 0.25
rpoB 762144 p.Glu780* stop_gained 0.17
rpoB 762477 p.Lys891Glu missense_variant 1.0
rpoB 762915 p.Ala1037Thr missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763289 c.-81C>A upstream_gene_variant 0.18
rpoC 765139 c.1770C>A synonymous_variant 0.23
rpoC 765848 p.Pro827Thr missense_variant 0.2
rpoC 766552 p.Phe1061Leu missense_variant 0.12
rpoC 767111 p.Leu1248Met missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775778 c.2703C>A synonymous_variant 0.22
mmpL5 775781 c.2700G>T synonymous_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776124 p.Leu786Pro missense_variant 0.12
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776666 p.Asp605Glu missense_variant 0.12
mmpL5 778678 c.-198C>A upstream_gene_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781501 c.-59C>A upstream_gene_variant 0.2
fbiC 1303702 p.Gly258Cys missense_variant 0.18
fbiC 1304348 p.Trp473Leu missense_variant 0.29
fbiC 1305014 p.Thr695Met missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406887 p.Leu152Met missense_variant 0.13
Rv1258c 1406915 c.426C>A synonymous_variant 0.2
Rv1258c 1406978 p.Met121Ile missense_variant 0.25
embR 1416791 p.Arg186Leu missense_variant 0.25
atpE 1461134 c.90C>A synonymous_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474644 n.987G>T non_coding_transcript_exon_variant 0.15
rrl 1476310 n.2653G>T non_coding_transcript_exon_variant 0.15
fabG1 1673887 p.Gln150Glu missense_variant 0.12
inhA 1674147 c.-55C>A upstream_gene_variant 0.2
inhA 1674420 p.Ser73Arg missense_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834291 p.Glu250Asp missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102245 c.798C>A synonymous_variant 0.17
ndh 2102253 p.Gly264Ser missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169912 p.Asn234Ser missense_variant 0.22
PPE35 2169953 c.660C>A synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518501 p.Met129Ile missense_variant 0.18
folC 2746857 p.Glu248* stop_gained 0.4
folC 2746930 c.669C>A synonymous_variant 0.25
pepQ 2859573 c.846C>A synonymous_variant 0.29
ribD 2986985 p.Leu49Phe missense_variant 0.29
Rv2752c 3064673 p.Ala507Thr missense_variant 0.14
Rv2752c 3065398 p.Ser265* stop_gained 0.18
Rv2752c 3065453 p.Gln247* stop_gained 1.0
Rv2752c 3066083 p.Leu37Met missense_variant 0.18
Rv2752c 3066127 p.Gly22Val missense_variant 0.12
Rv2752c 3066258 c.-67G>T upstream_gene_variant 0.17
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448861 p.Gly120Cys missense_variant 0.18
Rv3083 3449183 p.Ser227Tyr missense_variant 0.22
Rv3083 3449537 p.Ala345Val missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568736 c.-57T>G upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641499 p.Met319Ile missense_variant 0.29
fbiB 3641724 p.Pro64Thr missense_variant 0.29
alr 3840349 p.Ala358Thr missense_variant 0.14
ddn 3986886 p.Asp15Tyr missense_variant 0.25
clpC1 4039180 c.1524delG frameshift_variant 0.18
clpC1 4039586 c.1119G>T synonymous_variant 0.22
clpC1 4040165 c.540G>T synonymous_variant 0.22
clpC1 4040633 p.Asn24Lys missense_variant 0.13
embC 4239711 c.-152C>A upstream_gene_variant 0.2
embC 4241386 c.1524C>G synonymous_variant 0.17
embC 4241611 c.1749G>T synonymous_variant 0.18
embC 4241937 p.Arg692Met missense_variant 0.22
embA 4242367 c.-866C>A upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243355 c.123G>T synonymous_variant 0.22
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245343 p.Ser704* stop_gained 0.2
embA 4245878 p.Glu882Asp missense_variant 0.18
embA 4245975 p.Asp915Tyr missense_variant 0.29
embB 4246310 c.-204C>A upstream_gene_variant 0.17
embA 4246317 p.Pro1029Thr missense_variant 0.15
embB 4247083 c.570C>A synonymous_variant 0.15
embB 4247132 p.Asp207Tyr missense_variant 0.2
embB 4248939 p.Pro809His missense_variant 0.15
aftB 4267576 p.Ala421Ser missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268013 p.Pro275Gln missense_variant 0.18
ubiA 4269426 p.Leu136Phe missense_variant 0.17
aftB 4269576 c.-740C>A upstream_gene_variant 0.25
ethA 4326031 c.1443C>A synonymous_variant 0.15
ethA 4326851 p.Ser208Leu missense_variant 1.0
ethA 4326927 p.Ser183Arg missense_variant 0.37
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