TB-Profiler result

Run: ERR8665587
Summary

Run ID: ERR8665587

Sample name:

Date: 02-04-2023 07:32:55

Number of reads: 502516

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
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
pncA 2288954 p.Lys96Asn missense_variant 0.43 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.94 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
gyrA 7030 c.-272C>A upstream_gene_variant 0.15
gyrA 7313 c.12G>T synonymous_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8400 p.Asp367Tyr missense_variant 0.2
gyrA 8831 p.Leu510Phe missense_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9571 p.Arg757Leu missense_variant 0.17
gyrA 9582 p.Arg761Trp missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575369 p.Asp8Tyr missense_variant 0.22
mshA 575743 p.Phe132Leu missense_variant 0.25
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575910 p.Leu188Pro missense_variant 0.22
ccsA 619850 c.-41G>T upstream_gene_variant 0.33
ccsA 620427 c.537C>A synonymous_variant 0.17
ccsA 620619 c.729G>T synonymous_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760420 p.Trp205Leu missense_variant 0.2
rpoB 761567 p.Met587Ile missense_variant 0.18
rpoB 761689 p.Ala628Glu missense_variant 0.18
rpoB 762477 p.Lys891Glu missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764185 c.816C>A synonymous_variant 0.2
rpoC 764839 c.1470C>A synonymous_variant 0.18
rpoC 765413 p.Pro682Thr missense_variant 0.2
rpoC 765820 c.2451G>T synonymous_variant 0.25
rpoC 766252 p.Lys961Asn missense_variant 0.13
rpoC 766459 c.3090G>T synonymous_variant 0.18
rpoC 767237 p.Asp1290Asn missense_variant 0.13
mmpL5 775587 c.2894G>T stop_lost&splice_region_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777211 p.Asp424Tyr missense_variant 0.17
mmpR5 779258 p.Arg90Leu missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781607 c.48C>A synonymous_variant 0.15
rpsL 781635 p.Gly26Arg missense_variant 0.13
fbiC 1304810 p.Ser627Tyr missense_variant 0.17
Rv1258c 1406104 c.1237C>A synonymous_variant 0.2
Rv1258c 1406402 c.939C>A synonymous_variant 0.17
Rv1258c 1406660 c.681C>A synonymous_variant 0.29
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407386 c.-46C>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476248 n.2591G>T non_coding_transcript_exon_variant 0.18
inhA 1674726 c.525G>T synonymous_variant 0.22
rpsA 1833515 c.-27C>A upstream_gene_variant 0.18
rpsA 1833950 p.Gly137Cys missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917947 p.Arg3Leu missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102727 p.His106Asn missense_variant 0.23
ndh 2103074 c.-32C>G upstream_gene_variant 0.1
katG 2154626 p.Arg496Ser missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154941 p.Glu391* stop_gained 0.29
katG 2155017 c.1095G>T synonymous_variant 0.15
katG 2155173 c.939C>A synonymous_variant 0.2
katG 2155275 c.837C>A synonymous_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>T synonymous_variant 0.17
Rv1979c 2222232 c.933G>T synonymous_variant 0.2
Rv1979c 2223250 c.-86C>A upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289709 c.-468G>T upstream_gene_variant 0.33
kasA 2518330 p.Met72Ile missense_variant 0.25
eis 2714825 p.Glu170* stop_gained 0.18
ahpC 2726037 c.-156G>T upstream_gene_variant 0.17
ribD 2987466 p.Glu210* stop_gained 0.4
ribD 2987515 p.Arg226His missense_variant 0.33
Rv2752c 3065235 c.957G>T synonymous_variant 0.2
Rv2752c 3065453 p.Gln247* stop_gained 1.0
Rv2752c 3067130 c.-939G>T upstream_gene_variant 0.14
thyA 3073832 p.Glu214* stop_gained 0.23
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 0.14
fbiD 3339294 c.177C>A synonymous_variant 0.18
fbiD 3339470 p.Pro118Gln missense_variant 0.25
Rv3083 3449109 c.606C>A synonymous_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474670 p.Asp222Tyr missense_variant 0.25
fprA 3474775 p.Asp257Tyr missense_variant 0.29
fprA 3474794 p.Gly263Val missense_variant 0.25
whiB7 3568521 p.Leu53Phe missense_variant 0.17
whiB7 3568735 c.-56G>T upstream_gene_variant 0.15
whiB7 3568736 c.-57T>G upstream_gene_variant 1.0
Rv3236c 3612270 p.Asp283Tyr missense_variant 0.33
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641196 c.-339C>A upstream_gene_variant 0.2
rpoA 3878423 p.Gly29* stop_gained 0.14
ddn 3986877 p.Pro12Ser missense_variant 0.15
clpC1 4038234 p.Arg824Pro missense_variant 0.18
clpC1 4039917 p.Gly263Val missense_variant 0.25
clpC1 4039926 p.Arg260Leu missense_variant 0.25
clpC1 4039994 p.Glu237Asp missense_variant 0.18
clpC1 4040521 p.Gln62Lys missense_variant 0.18
panD 4044122 c.160C>A synonymous_variant 0.2
panD 4044436 c.-155C>A upstream_gene_variant 0.18
panD 4044437 c.-156C>T upstream_gene_variant 0.18
embA 4242352 c.-881G>T upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243586 p.Phe118Leu missense_variant 0.25
embA 4243631 c.399G>T synonymous_variant 0.29
embA 4244201 p.Trp323Cys missense_variant 0.33
embA 4244231 c.999C>A synonymous_variant 0.4
embA 4245982 p.Gly917Val missense_variant 0.33
embB 4249652 p.His1047Asn missense_variant 0.15
embB 4249797 p.Arg1095Leu missense_variant 0.27
aftB 4267088 c.1749C>A synonymous_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268201 c.636G>T synonymous_variant 0.27
ethA 4326851 p.Ser208Leu missense_variant 1.0
ethA 4326927 p.Ser183Arg missense_variant 0.42
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