TB-Profiler result

Run: ERR8665599
Summary

Run ID: ERR8665599

Sample name:

Date: 02-04-2023 07:33:21

Number of reads: 482920

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 0.99
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.Asp94Gly 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
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247586 p.Gly358Val missense_variant 0.15 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7486 p.Ser62Tyr missense_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491783 p.Arg334Leu missense_variant 0.2
mshA 575608 p.Glu87Asp missense_variant 0.17
mshA 575830 c.483C>A synonymous_variant 0.2
mshA 575832 p.Gly162Val missense_variant 0.2
mshA 575857 c.510G>T synonymous_variant 0.2
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576721 p.Glu458Asp missense_variant 0.22
ccsA 620018 p.Gly43Val missense_variant 0.33
ccsA 620582 p.Arg231Leu missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759661 c.-146G>T upstream_gene_variant 0.15
rpoB 759967 p.Ser54* stop_gained 0.22
rpoB 760069 p.Ser88Tyr missense_variant 0.18
rpoB 760177 p.Ala124Val missense_variant 0.17
rpoB 760424 c.618C>A synonymous_variant 0.22
rpoB 760645 p.Pro280His missense_variant 0.4
rpoB 760952 p.Gln382His missense_variant 0.25
rpoB 761184 p.Glu460* stop_gained 0.4
rpoB 762566 p.Met920Ile missense_variant 0.29
rpoB 762941 p.Met1045Ile missense_variant 0.21
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763284 p.Leu1160Met missense_variant 0.18
rpoC 763419 p.Ala17Glu missense_variant 0.14
rpoC 763626 p.Lys86Met missense_variant 0.15
rpoC 764311 c.942C>A synonymous_variant 0.25
rpoC 764981 p.Gly538Arg missense_variant 0.18
rpoC 766974 p.Ala1202Val missense_variant 0.2
rpoC 767010 p.Ser1214* stop_gained 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779418 p.Leu143Phe missense_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779621 c.-716G>T upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800763 c.-46C>A upstream_gene_variant 0.2
fbiC 1302918 c.-13A>G upstream_gene_variant 0.13
fbiC 1303150 p.Gly74Cys missense_variant 0.18
fbiC 1303800 c.870G>T synonymous_variant 0.25
Rv1258c 1406120 c.1221C>A synonymous_variant 0.2
Rv1258c 1406180 c.1161C>A synonymous_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472760 n.915G>T non_coding_transcript_exon_variant 0.19
inhA 1673643 c.-559C>G upstream_gene_variant 0.4
inhA 1673781 c.-421C>A upstream_gene_variant 0.17
inhA 1673844 c.-358G>T upstream_gene_variant 0.22
inhA 1674608 p.Pro136Gln missense_variant 0.25
rpsA 1833751 c.210C>A synonymous_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834270 c.729G>A synonymous_variant 0.18
rpsA 1834612 c.1071G>T synonymous_variant 0.2
rpsA 1834738 c.1197A>G synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102165 p.Ser293* stop_gained 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154822 c.1290G>T synonymous_variant 0.2
katG 2155238 p.Pro292Thr missense_variant 0.25
katG 2155347 p.Met255Ile missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170465 p.Ala50Thr missense_variant 0.2
PPE35 2170516 p.Gly33Trp missense_variant 0.33
PPE35 2170571 p.Leu14Phe missense_variant 0.22
Rv1979c 2222856 c.309C>A synonymous_variant 0.19
Rv1979c 2223239 c.-75G>T upstream_gene_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518215 p.Lys34Arg missense_variant 0.22
eis 2714838 p.Leu165Phe missense_variant 0.15
pepQ 2859609 c.810G>T synonymous_variant 0.18
ribD 2986724 c.-115C>A upstream_gene_variant 0.29
ribD 2986929 p.Leu31Phe missense_variant 0.22
ribD 2987606 c.768C>A synonymous_variant 0.4
Rv2752c 3065413 p.Ser260* stop_gained 0.2
Rv2752c 3065877 c.315G>T synonymous_variant 0.29
thyX 3067282 p.Val222Leu missense_variant 0.2
thyX 3067320 p.Arg209Leu missense_variant 0.2
thyA 3073833 c.639C>A synonymous_variant 0.29
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339112 c.-6G>T upstream_gene_variant 0.2
Rv3083 3448728 c.225C>A synonymous_variant 0.27
Rv3083 3449073 c.570C>A synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474103 p.Asp33Tyr missense_variant 0.22
fprA 3474288 c.282C>A synonymous_variant 0.29
whiB7 3568649 p.Pro11Thr missense_variant 0.18
whiB7 3568795 c.-116A>G upstream_gene_variant 1.0
Rv3236c 3612360 p.Gly253Trp missense_variant 0.5
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612932 p.Ala62Val missense_variant 0.22
fbiB 3641508 c.-27C>A upstream_gene_variant 0.27
fbiB 3641545 p.Pro4His missense_variant 0.17
fbiB 3642128 p.Ile198Met missense_variant 0.22
alr 3840248 c.1173C>A synonymous_variant 0.18
alr 3840738 p.Arg228Leu missense_variant 0.2
alr 3840790 p.Gln211Lys missense_variant 0.18
alr 3841210 p.Gly71Cys missense_variant 0.18
rpoA 3877892 p.Asp206Tyr missense_variant 0.2
clpC1 4038203 p.Lys834Asn missense_variant 0.29
clpC1 4039291 p.Asp472Tyr missense_variant 0.2
clpC1 4040835 c.-131G>T upstream_gene_variant 0.18
embC 4239950 c.88C>A synonymous_variant 0.2
embC 4242016 p.Phe718Leu missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243226 c.-7G>T upstream_gene_variant 0.25
embA 4243294 p.Gly21Val missense_variant 0.4
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243886 p.Met218Ile missense_variant 0.22
embA 4244071 p.Val280Ala missense_variant 0.12
embA 4244888 c.1656G>T synonymous_variant 0.18
embA 4245868 p.Ser879Tyr missense_variant 0.22
embB 4249492 c.2979C>A synonymous_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269974 c.-141C>A upstream_gene_variant 0.13
ethR 4328035 p.Pro163Thr missense_variant 0.18
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