TB-Profiler result

Run: ERR8665583
Summary

Run ID: ERR8665583

Sample name:

Date: 02-04-2023 07:32:45

Number of reads: 470619

Percentage reads mapped: 99.56

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 1.0 pyrazinamide
ahpC 2726142 c.-51G>T upstream_gene_variant 0.2 isoniazid
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 6706 p.Glu489Asp missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8114 c.813C>A synonymous_variant 0.2
gyrA 8273 c.972C>A synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490819 p.Glu13* stop_gained 0.33
fgd1 491140 p.Gly120Cys missense_variant 0.33
fgd1 491296 p.Val172Ile missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576502 c.1155C>T synonymous_variant 0.22
ccsA 619938 p.Trp16Cys missense_variant 0.14
ccsA 619960 p.Ala24Ser missense_variant 0.13
ccsA 620268 c.378G>A synonymous_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760648 p.Pro281Gln missense_variant 0.17
rpoB 762206 c.2400C>A synonymous_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764853 p.Pro495Gln missense_variant 0.17
rpoC 765247 c.1878C>A synonymous_variant 0.18
rpoC 766045 p.Gln892His missense_variant 0.25
rpoC 766083 p.Ala905Val missense_variant 0.2
rpoC 767001 p.Thr1211Lys missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775676 p.Lys935Asn missense_variant 0.29
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776642 p.Met613Ile missense_variant 0.17
mmpL5 776738 c.1743C>A synonymous_variant 0.18
mmpL5 777016 p.Gly489Cys missense_variant 0.2
mmpL5 777026 c.1455C>A synonymous_variant 0.14
mmpR5 778178 c.-812G>T upstream_gene_variant 0.2
mmpL5 779241 c.-761C>T upstream_gene_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800627 c.-182C>T upstream_gene_variant 0.14
rplC 800757 c.-52G>A upstream_gene_variant 0.25
rplC 801291 p.Phe161Leu missense_variant 0.18
rplC 801409 p.Arg201Ser missense_variant 0.18
fbiC 1303157 p.His76Arg missense_variant 0.15
Rv1258c 1406733 p.Ser203* stop_gained 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406976 p.Thr122Met missense_variant 0.18
embR 1416559 p.Lys263Asn missense_variant 0.2
embR 1417262 p.Pro29Gln missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475118 n.1461C>A non_coding_transcript_exon_variant 0.17
inhA 1673967 c.-235G>T upstream_gene_variant 1.0
inhA 1674653 p.Pro151Gln missense_variant 0.18
rpsA 1833992 p.Ser151Ala missense_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834216 p.Phe225Leu missense_variant 0.22
rpsA 1834660 p.Phe373Leu missense_variant 0.18
rpsA 1834676 p.Gly379Ser missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917977 p.Arg13Leu missense_variant 0.4
tlyA 1918243 p.Asp102Tyr missense_variant 0.2
ndh 2102410 c.633G>T synonymous_variant 0.4
katG 2154255 c.1857C>A synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154753 c.1359C>A synonymous_variant 0.21
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168386 p.Glu743* stop_gained 0.18
PPE35 2169200 c.1413G>T synonymous_variant 0.17
PPE35 2170602 p.Ser4* stop_gained 0.15
Rv1979c 2222140 p.Arg342Leu missense_variant 0.29
Rv1979c 2223132 c.33C>A synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288716 p.Arg176Ser missense_variant 0.25
pncA 2289249 c.-8G>T upstream_gene_variant 0.14
pncA 2289771 c.-530C>A upstream_gene_variant 0.25
kasA 2518555 c.441C>A synonymous_variant 0.18
kasA 2518789 c.675G>T synonymous_variant 0.22
eis 2714252 p.Leu361Ile missense_variant 0.14
eis 2715123 c.210G>T synonymous_variant 0.17
ahpC 2726074 c.-119C>A upstream_gene_variant 0.14
folC 2746455 c.1144C>T synonymous_variant 0.4
pepQ 2859601 c.817delG frameshift_variant 0.22
ribD 2986866 p.Ala10Ser missense_variant 0.17
ribD 2987529 p.Pro231Ser missense_variant 0.29
thyX 3067205 c.741G>T synonymous_variant 0.22
thyX 3067331 p.Asp205Glu missense_variant 0.2
thyX 3067720 p.Ala76Ser missense_variant 0.18
thyA 3073958 p.Leu172Met missense_variant 0.17
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087234 c.415C>A synonymous_variant 0.22
Rv3083 3448320 c.-184G>T upstream_gene_variant 0.18
Rv3083 3448367 c.-137G>T upstream_gene_variant 0.17
Rv3083 3448468 c.-36C>A upstream_gene_variant 0.2
Rv3083 3448663 p.Arg54Ser missense_variant 0.18
Rv3083 3449879 p.Pro459Gln missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568574 p.Leu36Ile missense_variant 0.17
whiB7 3568795 c.-116A>G upstream_gene_variant 1.0
Rv3236c 3612678 p.Glu147* stop_gained 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613037 p.Arg27Pro missense_variant 0.33
fbiB 3641981 c.447C>A synonymous_variant 0.29
alr 3840485 c.936C>A synonymous_variant 0.19
alr 3841405 p.Glu6* stop_gained 0.2
rpoA 3877774 p.Ala245Glu missense_variant 0.25
ddn 3987185 c.342G>T synonymous_variant 0.19
clpC1 4040894 c.-190G>T upstream_gene_variant 0.22
panD 4043994 c.288C>A synonymous_variant 0.25
embC 4241056 c.1194C>A synonymous_variant 0.25
embC 4242587 p.Gly909Arg missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243172 c.-61G>T upstream_gene_variant 0.2
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244115 c.883C>A synonymous_variant 0.29
embA 4245507 p.Gly759* stop_gained 0.17
embA 4246009 p.Arg926Leu missense_variant 0.29
embB 4248331 p.Met606Ile missense_variant 0.29
embB 4249583 p.Asp1024Tyr missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268749 p.Asp30Tyr missense_variant 0.2
ethA 4326960 p.Asp172Tyr missense_variant 0.2
ethA 4327355 p.Ser40Tyr missense_variant 0.22
ethR 4327934 p.Ala129Glu missense_variant 0.25
ethR 4327961 p.Trp138Leu missense_variant 0.29
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 4407768 p.Leu145Phe missense_variant 0.15
gid 4407827 p.Asp126Tyr missense_variant 0.2
gid 4407927 p.Glu92Asp missense_variant 1.0