TB-Profiler result

Run: ERR5865378
Summary

Run ID: ERR5865378

Sample name:

Date: 01-04-2023 23:59:09

Number of reads: 2201718

Percentage reads mapped: 63.01

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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu 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 2289001 p.Phe81Val missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326855 p.Arg207Gly missense_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 762899 c.-471G>C upstream_gene_variant 0.13
rpoC 762920 c.-450C>T upstream_gene_variant 0.12
rpoB 762925 p.Thr1040Ile missense_variant 0.11
rpoC 762929 c.-441G>C upstream_gene_variant 0.11
rpoC 762932 c.-438G>C upstream_gene_variant 0.11
rpoB 762939 p.Met1045Leu missense_variant 0.12
rpoB 762942 p.Ile1046Val missense_variant 0.11
rpoC 762980 c.-390T>C upstream_gene_variant 0.19
rpoC 762989 c.-381G>C upstream_gene_variant 0.15
rpoC 762995 c.-375G>T upstream_gene_variant 0.13
rpoC 762998 c.-372G>A upstream_gene_variant 0.11
rpoC 763028 c.-342T>C upstream_gene_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764575 c.1206T>G synonymous_variant 0.12
rpoC 764581 c.1212T>C synonymous_variant 0.12
rpoC 764582 p.Leu405Met missense_variant 0.12
rpoC 764605 c.1236G>C synonymous_variant 0.17
rpoC 764611 c.1242G>C synonymous_variant 0.15
rpoC 764632 c.1263T>C synonymous_variant 0.18
rpoC 764641 c.1272C>T synonymous_variant 0.19
rpoC 764650 c.1281G>T synonymous_variant 0.2
rpoC 764663 p.Val432Thr missense_variant 0.13
rpoC 764672 p.Gln435Glu missense_variant 0.11
rpoC 764817 p.Val483Gly missense_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 0.97
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 1472172 n.327T>C non_coding_transcript_exon_variant 0.11
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.12
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.12
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.12
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.12
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.12
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.12
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.11
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.11
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.12
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.12
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.26
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.33
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.33
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.32
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.34
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.34
rrl 1476381 n.2724G>A non_coding_transcript_exon_variant 0.35
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.34
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.38
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.39
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.21
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.18
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.17
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.15
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.11
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
thyA 3073715 p.Pro253Ala missense_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 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly 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