TB-Profiler result

Run: ERR5864927
Summary

Run ID: ERR5864927

Sample name:

Date: 01-04-2023 23:41:08

Number of reads: 3221619

Percentage reads mapped: 62.07

Strain: lineage2.2.1

Drug-resistance: MDR-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
rpoB 761155 p.Ser450Leu 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
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326463 c.1010delT 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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575688 c.345delG frameshift_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761277 p.Ile491Val missense_variant 0.8
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
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801433 p.Arg209Cys missense_variant 0.13
Rv1258c 1406102 c.1239G>A synonymous_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416965 p.Ala128Gly missense_variant 0.14
embR 1416968 p.Ala127Gly missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.12
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.1
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.12
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.1
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.1
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.1
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.1
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.11
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.1
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.24
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.11
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.12
rrs 1473201 n.1357C>T non_coding_transcript_exon_variant 0.14
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.12
rrl 1474240 n.583G>T non_coding_transcript_exon_variant 0.18
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.11
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.12
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.12
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.14
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.15
rrl 1475417 n.1760G>T non_coding_transcript_exon_variant 0.14
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.12
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.14
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.14
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.14
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.18
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.13
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.12
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.12
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.12
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.12
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.12
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.12
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.13
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15
rrl 1476535 n.2878G>A non_coding_transcript_exon_variant 0.14
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.18
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.18
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.17
rrl 1476580 n.2923G>A non_coding_transcript_exon_variant 0.22
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
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
aftB 4267647 p.Asp397Gly missense_variant 1.0
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