TB-Profiler result

Run: ERR4827437
Summary

Run ID: ERR4827437

Sample name:

Date: 01-04-2023 18:02:40

Number of reads: 581654

Percentage reads mapped: 99.33

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.Asp94Gly missense_variant 0.47 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761140 p.His445Arg 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289150 p.Ile31Ser missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4327132 c.341delA 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 5468 p.Val77Leu missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8298 p.Lys333Glu missense_variant 0.12
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
rpoC 765050 p.Ser561Pro missense_variant 1.0
rpoC 766482 p.Arg1038Leu 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
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476118 n.2461G>T non_coding_transcript_exon_variant 0.15
rrl 1476157 n.2500T>A non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.37
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155472 p.Arg214Trp missense_variant 0.12
PPE35 2167745 p.Thr956Arg missense_variant 0.12
PPE35 2167760 c.2853G>A synonymous_variant 0.13
PPE35 2167763 p.Ile950Val missense_variant 0.13
PPE35 2167780 p.Asn945Asp missense_variant 0.14
PPE35 2167865 c.2748G>C synonymous_variant 0.23
PPE35 2167868 c.2745A>C synonymous_variant 0.23
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168344 p.Gly757Ser missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.69
PPE35 2170053 p.Thr187Ser missense_variant 0.74
PPE35 2170157 c.456G>T synonymous_variant 0.12
PPE35 2170169 c.444A>G synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288762 c.480A>G synonymous_variant 0.12
pncA 2289254 c.-13G>T upstream_gene_variant 0.22
eis 2714582 p.Ala251Ser missense_variant 0.14
ahpC 2726716 p.Ala175Glu missense_variant 0.2
folC 2747791 c.-193T>A upstream_gene_variant 0.18
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3065256 p.Met312Ile missense_variant 0.14
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087826 p.Asn336Ser missense_variant 0.12
Rv3083 3449696 p.Lys398Arg missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474158 p.Ser51Phe missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640550 p.Val3Ala missense_variant 0.14
fbiB 3641944 p.Arg137Leu missense_variant 0.15
rpoA 3878055 c.453A>G synonymous_variant 0.12
rpoA 3878228 p.Thr94Ala missense_variant 0.11
clpC1 4039744 p.Gly321Ser missense_variant 0.18
embC 4240478 p.Gly206Arg missense_variant 0.29
embC 4240801 c.939C>T synonymous_variant 0.14
embC 4240803 p.Tyr314Phe missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242944 p.Asn1028Asp missense_variant 0.12
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243356 p.Thr42Ala missense_variant 0.22
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244550 p.Ala440Thr missense_variant 0.18
embB 4246544 p.Thr11Pro missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.38
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4249698 p.Gly1062Val missense_variant 0.5
aftB 4267647 p.Asp397Gly missense_variant 0.96
ethA 4326608 p.Trp289Leu missense_variant 0.14
ethR 4327366 c.-183T>C upstream_gene_variant 0.18
ethR 4327799 p.Asp84Gly missense_variant 0.12
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338585 c.-64G>A upstream_gene_variant 0.13
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