TB-Profiler result

Run: ERR5865290
Summary

Run ID: ERR5865290

Sample name:

Date: 01-04-2023 23:55:09

Number of reads: 489085

Percentage reads mapped: 99.52

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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2154301 c.1809_1810delGT frameshift_variant 0.2 isoniazid
katG 2155167 p.Ser315Thr missense_variant 0.29 isoniazid
pncA 2288952 p.Gly97Asp missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val 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 6303 p.Ala355Asp missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7587 p.Leu96Met missense_variant 0.15
gyrA 7593 p.Arg98Cys missense_variant 0.15
gyrA 8853 p.Val518Phe missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9675 p.Arg792Ser missense_variant 0.17
gyrA 9783 p.Val828Met missense_variant 0.13
fgd1 490697 c.-86C>A upstream_gene_variant 0.22
fgd1 490791 c.9A>G synonymous_variant 0.22
fgd1 490816 p.Ala12Ser missense_variant 0.18
fgd1 490956 p.Met58Ile missense_variant 0.33
fgd1 491053 p.Ala91Ser missense_variant 0.25
fgd1 491173 c.391C>A synonymous_variant 0.14
fgd1 491280 c.498C>A synonymous_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491764 p.Leu328Met missense_variant 0.14
mshA 575665 c.318G>T synonymous_variant 0.18
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576671 c.1324C>A synonymous_variant 0.22
mshA 576696 p.Ala450Asp missense_variant 0.2
ccsA 620106 p.Phe72Leu missense_variant 0.18
ccsA 620560 c.673dupC frameshift_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761009 p.Gln401His missense_variant 0.13
rpoB 762032 c.2227delT frameshift_variant 0.14
rpoB 762286 p.Arg827His missense_variant 1.0
rpoC 762899 c.-471G>T upstream_gene_variant 0.25
rpoB 762903 p.Asp1033Tyr missense_variant 0.25
rpoB 763009 p.Trp1068* stop_gained 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763136 c.-234C>A upstream_gene_variant 0.4
rpoC 763310 c.-60C>A upstream_gene_variant 0.22
rpoC 763582 p.Lys71Asn missense_variant 0.14
rpoC 765191 p.Glu608* stop_gained 0.17
rpoC 765940 c.2571A>G synonymous_variant 0.14
rpoC 766228 p.Leu953Phe missense_variant 0.14
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 767299 c.3930C>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775694 c.2787C>A synonymous_variant 0.29
mmpL5 775728 p.Thr918Asn missense_variant 0.33
mmpL5 776079 p.Ala801Asp missense_variant 0.22
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776656 p.Gly609* stop_gained 0.17
mmpL5 777315 p.Trp389* stop_gained 0.22
mmpL5 778916 c.-436G>T upstream_gene_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304141 p.Ala404Glu missense_variant 0.14
fbiC 1304144 p.Trp405Leu missense_variant 0.14
fbiC 1304185 p.Asp419Tyr missense_variant 0.15
fbiC 1304617 c.1687C>A synonymous_variant 0.17
fbiC 1304639 p.Arg570Leu missense_variant 0.22
fbiC 1304959 p.Arg677Ser missense_variant 0.2
fbiC 1304970 c.2040G>T synonymous_variant 0.22
fbiC 1305277 p.His783Tyr missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417230 p.Ala40Pro missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471843 n.-3G>T upstream_gene_variant 0.17
rrs 1473334 n.1489C>A non_coding_transcript_exon_variant 0.29
rrl 1473860 n.203C>A non_coding_transcript_exon_variant 0.67
rrl 1476360 n.2703C>A non_coding_transcript_exon_variant 0.67
inhA 1673967 c.-235G>T upstream_gene_variant 0.19
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917849 c.-91G>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102157 p.Glu296* stop_gained 0.18
ndh 2102243 p.Arg267Leu missense_variant 0.18
ndh 2102375 p.Pro223Gln missense_variant 0.15
ndh 2103034 c.9C>A synonymous_variant 0.13
ndh 2103087 c.-45A>G upstream_gene_variant 0.12
katG 2154163 p.Ser650Tyr missense_variant 0.2
katG 2154693 c.1419T>C synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155238 p.Pro292Thr missense_variant 0.17
katG 2155781 p.Gly111Cys missense_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168044 p.Ala857Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289345 c.-104G>T upstream_gene_variant 0.14
pncA 2290109 c.-868C>A upstream_gene_variant 0.17
kasA 2518424 p.Asp104Tyr missense_variant 0.33
kasA 2518600 c.486C>T synonymous_variant 0.4
eis 2714879 p.Asp152Tyr missense_variant 0.17
ahpC 2726405 c.213C>G synonymous_variant 0.2
folC 2746249 c.1350C>A synonymous_variant 0.2
folC 2746998 p.His201Asn missense_variant 0.4
pepQ 2859453 c.966G>T synonymous_variant 0.18
pepQ 2860044 c.375C>T synonymous_variant 0.17
pepQ 2860167 c.252C>A synonymous_variant 0.18
pepQ 2860302 c.117C>A synonymous_variant 0.25
pepQ 2860437 c.-19G>T upstream_gene_variant 0.15
ribD 2987214 c.378delT frameshift_variant 0.29
Rv2752c 3065704 p.Gly163Val missense_variant 0.17
Rv2752c 3067060 c.-869C>A upstream_gene_variant 0.2
thyX 3067604 c.342G>T synonymous_variant 0.29
thyX 3067706 p.Phe80Leu missense_variant 0.33
thyX 3067910 c.36C>A synonymous_variant 0.18
thyX 3067939 p.Glu3* stop_gained 0.17
thyX 3068094 c.-149A>G upstream_gene_variant 0.22
thyA 3073790 p.Pro228Thr missense_variant 0.33
thyA 3074002 p.Gly157Val missense_variant 0.14
thyA 3074122 p.Asp117Gly missense_variant 0.18
ald 3086752 c.-68C>A upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087846 p.Leu343Ile missense_variant 0.13
Rv3083 3448416 c.-88C>T upstream_gene_variant 0.12
Rv3083 3448554 c.51C>A synonymous_variant 0.18
Rv3083 3448806 c.303C>A synonymous_variant 0.2
Rv3083 3449376 c.873G>A synonymous_variant 0.29
Rv3083 3449728 p.Leu409Met missense_variant 0.17
fprA 3473908 c.-99C>A upstream_gene_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474398 p.Trp131Leu missense_variant 0.22
fprA 3474681 c.675C>T synonymous_variant 0.18
fprA 3475227 c.1221C>A synonymous_variant 0.17
Rv3236c 3612031 p.Met362Ile missense_variant 0.17
Rv3236c 3612409 c.708G>T synonymous_variant 0.17
Rv3236c 3612734 p.Ser128Tyr missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612981 p.Gly46Cys missense_variant 0.14
Rv3236c 3613102 p.Arg5Ser missense_variant 0.18
fbiA 3640754 p.Gly71Val missense_variant 0.2
fbiB 3641637 p.Ala35Ser missense_variant 0.18
fbiB 3641926 p.Thr131Asn missense_variant 0.18
fbiB 3642161 c.627G>T synonymous_variant 0.17
alr 3841362 p.Thr20Lys missense_variant 0.14
alr 3841432 c.-12G>T upstream_gene_variant 0.14
rpoA 3878505 c.3G>T start_lost 0.27
ddn 3986737 c.-107G>T upstream_gene_variant 0.12
ddn 3986834 c.-10G>T upstream_gene_variant 0.21
ddn 3987272 c.429G>T synonymous_variant 0.25
clpC1 4038266 c.2439C>A synonymous_variant 0.15
clpC1 4040424 p.Glu94Gly missense_variant 0.12
embC 4240528 p.Tyr222* stop_gained 0.2
embC 4240957 c.1095C>A synonymous_variant 0.18
embC 4241055 p.Pro398His missense_variant 0.13
embC 4241569 c.1707C>A synonymous_variant 0.2
embC 4242287 p.Leu809Ile missense_variant 0.22
embC 4242323 p.Gly821Cys missense_variant 0.14
embC 4242335 p.Gly825Cys missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243251 p.Glu7* stop_gained 0.29
embA 4243326 p.Pro32Thr missense_variant 0.15
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243946 c.714C>A synonymous_variant 0.22
embA 4244037 c.807delC frameshift_variant 0.18
embA 4244588 c.1356G>T synonymous_variant 0.17
embA 4244765 c.1533T>C synonymous_variant 0.17
embA 4245212 c.1980G>T synonymous_variant 0.14
embA 4245450 p.Leu740Met missense_variant 0.2
embA 4245625 p.Ser798Leu missense_variant 0.18
embB 4246648 c.135G>A synonymous_variant 0.22
embB 4246650 p.Leu46Pro missense_variant 0.22
embB 4247125 c.612G>T synonymous_variant 0.2
embB 4247151 p.Arg213Leu missense_variant 0.22
embB 4247644 c.1131G>T synonymous_variant 0.22
embB 4248253 c.1740C>A synonymous_variant 0.2
embB 4248280 c.1767C>A synonymous_variant 0.18
embB 4248909 p.Ala799Asp missense_variant 0.13
aftB 4267184 c.1653C>A synonymous_variant 0.22
aftB 4267349 p.Met496Ile missense_variant 0.18
aftB 4267454 p.Asp461Glu missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267652 p.Met395Ile missense_variant 0.15
aftB 4268105 c.732T>C synonymous_variant 0.11
aftB 4268470 p.Leu123Met missense_variant 0.17
ubiA 4268930 c.901_903delTTC conservative_inframe_deletion 0.15
ethA 4326713 p.Gln254Pro missense_variant 1.0
ethA 4327464 p.His4Asn missense_variant 0.29
ethR 4327570 p.Gln8Lys missense_variant 0.17
ethA 4328215 c.-742C>A upstream_gene_variant 0.13
ethA 4328258 c.-785G>T upstream_gene_variant 0.17
whiB6 4338231 c.291C>A synonymous_variant 0.15
whiB6 4338263 p.Ala87Thr missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407727 p.Met159Thr missense_variant 0.13
gid 4407809 p.Asp132Tyr missense_variant 0.17
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408196 p.Pro3Thr missense_variant 0.22