TB-Profiler result

Run: ERR4830888
Summary

Run ID: ERR4830888

Sample name:

Date: 01-04-2023 20:31:32

Number of reads: 2670067

Percentage reads mapped: 85.95

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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761128 p.Ser441Leu missense_variant 0.97 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.83 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.15 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
folC 2747480 p.Glu40Gly missense_variant 1.0 para-aminosalicylic_acid
embB 4249518 p.His1002Arg missense_variant 1.0 ethambutol
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 0.99
mshA 576108 p.Ala254Gly missense_variant 0.21
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_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
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.12
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.13
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.1
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.12
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.12
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.16
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.18
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.16
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.11
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.12
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.1
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.13
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.12
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.11
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.12
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.12
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.2
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.15
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.18
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.19
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.18
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.19
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.21
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.13
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.18
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.17
rrl 1474830 n.1173A>C non_coding_transcript_exon_variant 0.1
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.11
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.16
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.17
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.1
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.1
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.11
rrl 1476260 n.2603A>G 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
PPE35 2170065 p.Ala183Gly missense_variant 0.24
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289082 p.Pro54Ala missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.58
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326869 p.Val202Gly 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