TB-Profiler result

Run: ERR8665811
Summary

Run ID: ERR8665811

Sample name:

Date: 02-04-2023 07:40:26

Number of reads: 298846

Percentage reads mapped: 9.28

Strain: lineage2.2

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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
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 7581 p.Asp94Tyr 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
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 5357 p.Arg40Cys missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9173 c.1872G>A synonymous_variant 0.65
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
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 777015 p.Gly489Val missense_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406600 p.Phe247Leu missense_variant 0.67
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416802 c.546C>A synonymous_variant 0.33
embR 1416973 c.375G>T synonymous_variant 0.25
embR 1417298 p.Gly17Val missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.2
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.2
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.17
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.15
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.15
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.15
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.17
rrs 1472592 n.747C>T non_coding_transcript_exon_variant 0.18
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.2
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.2
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.2
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.18
rrs 1472698 n.853A>C non_coding_transcript_exon_variant 0.18
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.13
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.13
rrs 1472719 n.874G>A non_coding_transcript_exon_variant 0.13
rrs 1472733 n.888G>T non_coding_transcript_exon_variant 0.27
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.25
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.27
rrs 1472742 n.897C>A non_coding_transcript_exon_variant 0.27
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.24
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.25
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.24
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.15
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.18
rrl 1474858 n.1201C>A non_coding_transcript_exon_variant 0.25
rrl 1475428 n.1771G>A non_coding_transcript_exon_variant 0.14
rrl 1476381 n.2724G>A non_coding_transcript_exon_variant 0.18
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.27
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.36
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.4
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.57
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
inhA 1674914 c.715_716dupGC frameshift_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834181 p.Gly214Cys missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290104 c.-863G>T upstream_gene_variant 0.33
eis 2715261 p.Phe24Leu missense_variant 0.29
ribD 2986926 p.Gln30Lys missense_variant 0.22
ribD 2986967 c.129G>T synonymous_variant 0.22
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338999 c.-119T>C upstream_gene_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568795 c.-116A>G upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613023 p.Pro32Thr missense_variant 0.29
fbiA 3640844 p.Trp101Leu missense_variant 0.25
fbiB 3642273 p.Glu247Lys missense_variant 0.29
alr 3840377 c.1044C>A synonymous_variant 0.14
clpC1 4038515 p.Met730Ile missense_variant 0.4
clpC1 4038946 p.Asp587Tyr missense_variant 0.22
clpC1 4039697 c.1008C>A synonymous_variant 0.4
clpC1 4040454 p.Ala84Asp missense_variant 0.25
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 4244636 c.1404G>T synonymous_variant 0.33
embB 4249797 p.Arg1095Leu missense_variant 0.2
aftB 4266972 p.Gly622Asp missense_variant 0.29
aftB 4267458 p.Trp460Leu missense_variant 0.4
aftB 4269816 c.-980G>T upstream_gene_variant 0.17
ethA 4326306 p.Ser390Ala missense_variant 0.12
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