TB-Profiler result

Run: SRR11972436
Summary

Run ID: SRR11972436

Sample name:

Date: 03-04-2023 05:42:19

Number of reads: 758467

Percentage reads mapped: 83.6

Strain: lineage3.1.2

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
lineage3.1.2 East-African-Indian CAS;CAS2 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
mshA 575162 c.-186T>C upstream_gene_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761577 c.1771C>T synonymous_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766821 p.Asp1151Val missense_variant 0.12
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
rpsL 781757 p.Tyr66* stop_gained 0.12
fbiC 1305307 p.Val793Leu missense_variant 0.13
atpE 1461186 p.Arg48Trp missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.12
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.12
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.12
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.11
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.11
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.11
rrl 1475115 n.1458A>G non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.13
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.36
fabG1 1673990 p.Gly184Asp missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155717 p.Leu132Pro missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.31
PPE35 2170415 c.198A>G synonymous_variant 0.12
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
pncA 2289779 c.-539delC upstream_gene_variant 0.2
eis 2715060 p.His91Lys missense_variant 0.1
eis 2715065 p.Thr90Ala missense_variant 0.11
ahpC 2725929 c.-264C>G upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726213 c.21C>G synonymous_variant 0.1
ahpC 2726260 p.Leu23Gln missense_variant 0.17
pepQ 2859474 c.945A>T synonymous_variant 0.18
pepQ 2860092 c.325_326dupGC frameshift_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3987108 p.Tyr89Asp missense_variant 0.14
clpC1 4039180 p.Arg509Trp missense_variant 0.11
clpC1 4039406 c.1299G>A synonymous_variant 0.14
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
gid 4407806 p.Ala133Pro missense_variant 0.17