TB-Profiler result

Run: ERR2510354
Summary

Run ID: ERR2510354

Sample name:

Date: 31-03-2023 18:41:56

Number of reads: 1769250

Percentage reads mapped: 97.9

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 761140 p.His445Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 576108 p.Ala254Gly missense_variant 0.17
mshA 576482 p.Val379Leu missense_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759937 p.Val44Gly missense_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.12
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.13
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.13
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.12
rrs 1472970 n.1125C>A non_coding_transcript_exon_variant 0.12
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.12
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.12
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.13
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.13
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.12
rrs 1473001 n.1156G>C non_coding_transcript_exon_variant 0.13
rrs 1473002 n.1157G>A non_coding_transcript_exon_variant 0.13
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.13
rrs 1473008 n.1163C>T non_coding_transcript_exon_variant 0.13
rrs 1473009 n.1164T>G non_coding_transcript_exon_variant 0.12
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.14
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 2170048 p.Leu189Val missense_variant 0.27
PPE35 2170053 p.Thr187Ser missense_variant 0.29
PPE35 2170254 p.Leu120Arg missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A 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
fbiB 3642877 p.Lys448Arg missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243191 c.-41_-40delAT upstream_gene_variant 1.0
embA 4244744 c.1512C>T synonymous_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.15
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
embB 4246584 p.Arg24Pro missense_variant 0.38
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0