TB-Profiler result

Run: ERR5865400
Summary

Run ID: ERR5865400

Sample name:

Date: 01-04-2023 23:59:45

Number of reads: 549567

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
gyrB 6579 p.Ser447Phe 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
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155541 p.Trp191Arg missense_variant 0.12 isoniazid
pncA 2288792 c.449dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4327363 c.110delA 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9756 p.Ala819Ser missense_variant 0.19
fgd1 490787 p.Ala2Asp missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575769 p.Ala141Glu missense_variant 0.2
mshA 575773 c.426C>A synonymous_variant 0.2
mshA 575784 p.Gly146Val missense_variant 0.2
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576289 c.942G>T synonymous_variant 0.14
mshA 576346 p.His333Gln missense_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620637 c.747C>A synonymous_variant 0.33
ccsA 620833 p.Val315Ile missense_variant 0.22
rpoB 762747 p.Gly981Cys missense_variant 0.22
rpoB 762757 p.Ser984* stop_gained 0.22
rpoB 762792 p.Val996Ile missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765463 p.Asn698Lys missense_variant 1.0
rpoC 765521 p.Asp718Tyr missense_variant 0.25
rpoC 766390 c.3021C>G synonymous_variant 0.25
rpoC 766426 c.3057C>G synonymous_variant 0.18
rpoC 766834 p.Glu1155Asp missense_variant 0.22
rpoC 767255 p.Asp1296Tyr missense_variant 0.22
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 777094 c.1387T>C synonymous_variant 0.11
mmpL5 777152 p.Met443Ile missense_variant 0.18
mmpL5 777351 p.Arg377Gln missense_variant 0.15
mmpL5 777839 c.642G>T synonymous_variant 0.27
mmpL5 777900 p.Ala194Asp missense_variant 0.14
mmpL5 777971 p.Lys170Asn missense_variant 0.21
mmpL5 778033 p.Gln150Lys missense_variant 0.2
mmpL5 778344 p.Leu46Pro missense_variant 0.12
mmpS5 778556 p.Thr117Ser missense_variant 0.13
mmpS5 779565 c.-660G>T upstream_gene_variant 0.18
mmpS5 779567 c.-662G>T upstream_gene_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800753 c.-55delA upstream_gene_variant 0.17
rplC 801426 c.618C>A synonymous_variant 0.19
fbiC 1304272 p.Asp448Tyr missense_variant 0.2
fbiC 1304631 p.Phe567Leu missense_variant 0.22
fbiC 1304739 c.1809C>T synonymous_variant 0.22
fbiC 1304993 p.Ser688* stop_gained 0.18
Rv1258c 1406249 c.1092G>T synonymous_variant 0.12
Rv1258c 1406505 p.Ala279Asp missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406992 p.Gly117Cys missense_variant 0.2
embR 1417403 c.-56G>T upstream_gene_variant 0.21
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473371 n.1526C>A non_coding_transcript_exon_variant 0.22
rrl 1473717 n.60G>T non_coding_transcript_exon_variant 0.15
rrl 1474638 n.981C>A non_coding_transcript_exon_variant 0.17
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.2
inhA 1674391 p.Asp64Tyr missense_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834363 p.Leu274Phe missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918409 p.Phe157Ser missense_variant 0.12
ndh 2102108 p.Pro312His missense_variant 0.17
ndh 2102944 c.99C>A synonymous_variant 0.18
ndh 2103001 p.Arg14Ser missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155868 p.Glu82* stop_gained 0.18
katG 2155989 p.Asn41Lys missense_variant 0.2
katG 2156373 c.-262C>A upstream_gene_variant 0.22
PPE35 2167789 p.Gly942Cys missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168678 p.Ser645Arg missense_variant 0.2
PPE35 2169089 c.1524G>T synonymous_variant 0.16
Rv1979c 2222206 p.Ser320* stop_gained 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518139 p.Gly9Cys missense_variant 0.15
kasA 2519051 c.948_960delTATCGGCGACGCC frameshift_variant 0.25
eis 2715005 p.Asp110Tyr missense_variant 0.29
eis 2715313 p.Ser7Ile missense_variant 0.33
ahpC 2726596 p.Thr135Ile missense_variant 0.13
folC 2746237 c.1362G>T synonymous_variant 0.2
folC 2746257 p.Asp448Tyr missense_variant 0.25
folC 2746572 p.Arg343Ser missense_variant 0.15
folC 2747230 c.369C>A synonymous_variant 0.33
folC 2747291 p.Ser103* stop_gained 0.18
ribD 2986690 c.-149C>A upstream_gene_variant 0.2
Rv2752c 3065672 p.Asp174Tyr missense_variant 0.18
thyA 3074092 p.Arg127Leu missense_variant 0.18
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087018 p.Asp67His missense_variant 0.13
ald 3087685 p.Ala289Asp missense_variant 0.2
ald 3087690 p.His291Asn missense_variant 0.18
fbiD 3339324 c.207G>T synonymous_variant 0.17
Rv3083 3448357 c.-147C>A upstream_gene_variant 0.15
Rv3083 3448458 c.-46C>A upstream_gene_variant 0.2
Rv3083 3449011 p.Pro170Thr missense_variant 0.2
fprA 3473962 c.-45C>A upstream_gene_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474201 p.Lys65Asn missense_variant 0.33
fprA 3474260 p.Gly85Asp missense_variant 0.5
fprA 3474457 p.Val151Ile missense_variant 0.22
fprA 3475369 p.Leu455Ile missense_variant 0.4
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640685 p.Gly48Val missense_variant 0.25
fbiB 3642155 c.621C>A synonymous_variant 0.2
fbiB 3642396 p.Ala288Ser missense_variant 0.18
fbiB 3642410 c.876C>A synonymous_variant 0.2
alr 3840875 c.546C>A synonymous_variant 0.2
rpoA 3878169 c.339G>T synonymous_variant 0.15
clpC1 4039307 c.1397delA frameshift_variant 0.25
clpC1 4039520 c.1185G>T synonymous_variant 0.24
clpC1 4039943 c.762G>T synonymous_variant 0.15
embC 4239945 p.Ile28Asn missense_variant 0.18
embC 4240102 c.240C>A synonymous_variant 0.2
embC 4240549 c.687G>T synonymous_variant 0.2
embC 4241218 c.1356G>T synonymous_variant 0.18
embC 4241226 p.Pro455Gln missense_variant 0.2
embC 4241386 c.1524C>A synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242719 p.Ala953Ser missense_variant 0.25
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244514 p.Ala428Ser missense_variant 0.29
embA 4245526 p.Gly765Val missense_variant 0.18
embA 4245754 p.Gly841Asp missense_variant 0.2
embA 4246441 p.Pro1070Gln missense_variant 0.15
embB 4247770 c.1257C>A synonymous_variant 0.2
embB 4248874 c.2361C>A synonymous_variant 0.13
embB 4249007 p.Pro832Ser missense_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267785 p.Gly351Glu missense_variant 0.18
aftB 4269533 c.-697C>T upstream_gene_variant 0.13
ubiA 4269553 p.Ala94Asp missense_variant 0.14
ethR 4327270 c.-279G>T upstream_gene_variant 0.2
ethA 4327308 p.Asp56Tyr missense_variant 0.31
ethR 4327648 p.Glu34* stop_gained 0.25
ethR 4327859 p.Arg104Pro missense_variant 0.11
ethR 4327993 p.Thr149Ala missense_variant 0.13
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 4408165 p.Gly13Val missense_variant 0.15