TB-Profiler result

Run: SRR19392855
Summary

Run ID: SRR19392855

Sample name:

Date: 03-04-2023 21:36:56

Number of reads: 775125

Percentage reads mapped: 99.54

Strain: lineage3.1.1

Drug-resistance: Sensitive

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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
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili 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
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
rpoB 759711 c.-95_-88delGCCGAAAC upstream_gene_variant 0.25
rpoB 759723 c.-84C>T upstream_gene_variant 0.25
rpoB 759726 c.-81A>T upstream_gene_variant 0.25
rpoB 759727 c.-80A>T upstream_gene_variant 0.25
rpoB 759730 c.-77A>G upstream_gene_variant 0.2
rpoB 759733 c.-74_-73insGTTTCGGC upstream_gene_variant 0.2
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760415 c.609C>A synonymous_variant 0.13
rpoB 760460 c.654G>T synonymous_variant 0.12
rpoB 760689 p.Phe295Leu missense_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764940 p.Leu524Pro missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776114 c.2367C>T synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406349 p.Ile331Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472249 n.409delG non_coding_transcript_exon_variant 0.2
rrs 1472529 n.684G>T non_coding_transcript_exon_variant 0.13
rrs 1472740 n.895G>T non_coding_transcript_exon_variant 0.14
rrl 1473537 n.-121C>A upstream_gene_variant 0.13
rrl 1473747 n.90C>A non_coding_transcript_exon_variant 0.12
rrl 1473965 n.308G>A non_coding_transcript_exon_variant 0.2
rrl 1475258 n.1601T>C non_coding_transcript_exon_variant 0.18
rrl 1475975 n.2318C>A non_coding_transcript_exon_variant 0.15
rrl 1476740 n.3083G>A non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102518 c.525T>A synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169496 p.Asp373Asn missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.12
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859758 p.Asp221Asn missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0