TB-Profiler result

Run: ERR2041695
Summary

Run ID: ERR2041695

Sample name:

Date: 18-08-2022 09:23:06

Number of reads: 390927

Percentage reads mapped: 99.65

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
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 2289222 p.Val7Gly missense_variant 1.0 pyrazinamide
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 6112 p.Met291Ile missense_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7630 p.Val110Glu missense_variant 0.17
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
rpoB 760584 p.Asn260Tyr missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764916 p.Leu516Pro missense_variant 1.0
rpoC 765282 p.Thr638Asn missense_variant 0.12
rpoC 765517 c.2148C>T synonymous_variant 0.12
rpoC 765595 c.2226G>A synonymous_variant 0.11
rpoC 765667 p.Asn766Lys missense_variant 0.11
rpoC 766085 p.Pro906Thr missense_variant 0.12
rpoC 766333 c.2964G>A synonymous_variant 0.14
mmpR5 779206 p.Met73Val missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrl 1475519 n.1862G>A non_coding_transcript_exon_variant 0.14
rrl 1475855 n.2198A>G non_coding_transcript_exon_variant 0.11
fabG1 1673619 p.Cys60* stop_gained 0.12
inhA 1674156 c.-46C>T upstream_gene_variant 0.11
rpsA 1833359 c.-182delG upstream_gene_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834547 c.1007delA frameshift_variant 0.15
rpsA 1834902 p.Ala454Val missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154566 p.Lys516Glu missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155144 p.Asn323Ile missense_variant 0.14
kasA 2519043 p.Ala310Glu missense_variant 0.13
pepQ 2859766 p.Val218Ala missense_variant 0.12
ribD 2986918 p.Glu27Gly missense_variant 0.12
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiA 3641280 p.Ile246Met missense_variant 0.11
fbiB 3642478 p.Asp315Val missense_variant 0.12
alr 3841287 p.Ile45Thr missense_variant 0.2
embC 4239828 c.-35G>T upstream_gene_variant 0.11
embC 4239989 c.127C>T synonymous_variant 0.12
embC 4240073 c.212delA frameshift_variant 0.15
embC 4240856 p.Ala332Pro missense_variant 0.14
embC 4241565 p.Ile568Thr missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243123 c.-110T>C upstream_gene_variant 0.12
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244375 c.1143C>T synonymous_variant 0.11
embB 4247179 c.666C>T synonymous_variant 0.11
gid 4407588 c.615A>G synonymous_variant 1.0