TB-Profiler result

Run: ERR5863865
Summary

Run ID: ERR5863865

Sample name:

Date: 01-04-2023 22:57:26

Number of reads: 703224

Percentage reads mapped: 99.12

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 7563 p.Gly88Cys missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288820 p.Gln141Pro missense_variant 1.0 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491203 c.422delA frameshift_variant 0.12
fgd1 491286 c.504G>T synonymous_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575691 p.Gly115Val missense_variant 0.15
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576111 p.Ala255Asp missense_variant 0.17
mshA 576219 p.Pro291His missense_variant 0.18
mshA 576454 c.1107G>T synonymous_variant 0.17
mshA 576557 p.His404Asn missense_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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 777349 p.Gly378Cys missense_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302744 c.-187C>A upstream_gene_variant 0.18
fbiC 1302812 c.-119G>A upstream_gene_variant 0.14
fbiC 1303408 p.Glu160* stop_gained 0.2
fbiC 1303445 p.Ser172Tyr missense_variant 0.18
fbiC 1305313 p.Arg795Ser missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 0.93
Rv1258c 1407203 c.138C>A synonymous_variant 0.2
Rv1258c 1407381 c.-41G>T upstream_gene_variant 0.15
Rv1258c 1407401 c.-61G>T upstream_gene_variant 0.17
Rv1258c 1407403 c.-63G>T upstream_gene_variant 0.18
embR 1416481 c.867G>T synonymous_variant 0.17
embR 1417077 c.270delA frameshift_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472999 n.1154C>T non_coding_transcript_exon_variant 0.22
rrl 1473403 n.-255C>A upstream_gene_variant 0.25
fabG1 1673668 p.Glu77* stop_gained 0.18
rpsA 1833767 p.Pro76Thr missense_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917829 c.-111C>A upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917982 p.Gly15Cys missense_variant 0.16
tlyA 1918618 p.Ala227Ser missense_variant 0.18
tlyA 1918684 c.745C>A synonymous_variant 0.15
ndh 2101758 p.Leu429Met missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154770 p.Asp448Tyr missense_variant 0.2
katG 2154812 p.Gln434Lys missense_variant 0.17
katG 2156122 c.-11G>T upstream_gene_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167960 c.2652delG frameshift_variant 0.1
PPE35 2170331 c.282G>T synonymous_variant 0.15
Rv1979c 2221884 c.1281G>A synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518234 p.Glu40Asp missense_variant 0.29
ribD 2986810 c.-29C>A upstream_gene_variant 0.2
ribD 2987253 p.Ala139Ser missense_variant 0.15
Rv2752c 3065150 c.1041_1042insA frameshift_variant 1.0
Rv2752c 3067187 c.-997_-996insG upstream_gene_variant 1.0
thyX 3067234 p.Gly238Cys missense_variant 0.27
thyX 3067244 c.702C>T synonymous_variant 0.18
thyX 3067256 p.Phe230Leu missense_variant 0.25
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449560 p.Leu353Met missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474117 p.Asp37Glu missense_variant 0.13
whiB7 3568458 c.222C>A synonymous_variant 0.17
whiB7 3568508 p.Gln58Lys missense_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640600 p.Gln20Lys missense_variant 0.18
rpoA 3878256 c.252G>T synonymous_variant 0.17
rpoA 3878456 c.52C>A synonymous_variant 0.18
clpC1 4038679 p.Pro676Thr missense_variant 0.22
embC 4240980 p.Thr373Lys missense_variant 0.13
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 4243681 p.Ala150Asp missense_variant 0.12
embA 4245752 p.Met840Ile missense_variant 0.14
embA 4245882 p.Gly884Cys missense_variant 0.2
embB 4246427 c.-87G>T upstream_gene_variant 0.15
embB 4246920 p.Pro136Gln missense_variant 0.17
embB 4247043 p.Pro177His missense_variant 0.14
embB 4249731 p.Ala1073Gly missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267895 p.Phe314Leu missense_variant 0.18
aftB 4267970 p.Phe289Leu missense_variant 0.17
ubiA 4269893 c.-60G>T upstream_gene_variant 0.2
ubiA 4269995 c.-162C>A upstream_gene_variant 0.17
ethA 4328416 c.-945_-944delTG upstream_gene_variant 0.14
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 4407873 c.330G>T synonymous_variant 0.17
gid 4407927 p.Glu92Asp missense_variant 1.0