TB-Profiler result

Run: ERR2516270
Summary

Run ID: ERR2516270

Sample name:

Date: 31-03-2023 21:25:03

Number of reads: 1368295

Percentage reads mapped: 42.24

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
gyrB 6576 p.Arg446His 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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.94 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288929 p.Gly105Arg missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327333 c.140dupT frameshift_variant 1.0 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 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 777724 p.His253Asn missense_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304851 p.Gly641Cys missense_variant 0.67
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.22
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.23
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.23
rrs 1472575 n.730C>T non_coding_transcript_exon_variant 0.21
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.21
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.22
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.26
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.22
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.13
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.25
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.47
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.51
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.69
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.7
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.67
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.62
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.23
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.12
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.21
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.22
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.24
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.25
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.25
rrs 1473080 n.1235C>A non_coding_transcript_exon_variant 0.26
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.27
rrs 1473099 n.1254T>G non_coding_transcript_exon_variant 0.24
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.24
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.1
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
kasA 2519057 p.Thr315Ser missense_variant 0.12
kasA 2519062 c.948T>G synonymous_variant 0.13
folC 2746586 p.Arg338Leu missense_variant 0.12
ribD 2987307 p.Ala157Pro missense_variant 0.22
thyA 3073806 c.666C>G synonymous_variant 0.25
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
aftB 4268618 c.219G>T synonymous_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