TB-Profiler result

Run: SRR5341262
Summary

Run ID: SRR5341262

Sample name:

Date: 04-04-2023 10:11:35

Number of reads: 588636

Percentage reads mapped: 99.31

Strain: lineage3

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
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
gyrB 6412 p.Gln391His missense_variant 0.12
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 575737 c.390T>C synonymous_variant 0.1
rpoB 759620 c.-187A>C upstream_gene_variant 0.29
rpoB 759746 c.-61C>T upstream_gene_variant 0.88
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762952 p.Gln1049Arg missense_variant 0.11
rpoB 762955 p.Pro1050Leu missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766598 p.Tyr1077His missense_variant 0.14
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 1472653 n.808C>T non_coding_transcript_exon_variant 1.0
rrs 1473126 n.1282dupG non_coding_transcript_exon_variant 0.94
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673349 c.-91G>C upstream_gene_variant 0.12
fabG1 1673357 c.-83G>A upstream_gene_variant 0.18
fabG1 1673359 c.-81T>C upstream_gene_variant 0.18
fabG1 1673361 c.-79C>G upstream_gene_variant 0.19
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918034 p.Val32Gly missense_variant 0.22
ndh 2103225 c.-183A>C upstream_gene_variant 0.31
katG 2154604 p.Val503Ala missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.55
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
kasA 2518286 p.Val58Phe missense_variant 1.0
eis 2714380 c.952delT frameshift_variant 0.17
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyX 3067530 c.380_415delACCTGCGCCACATCCTGACCGAGGCCGCCGACGCCG disruptive_inframe_deletion 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475261 p.Thr419Ala missense_variant 0.18
alr 3841541 c.-121A>G upstream_gene_variant 0.14
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.27
embB 4246548 p.Pro12Gln missense_variant 0.47
embB 4246555 c.42G>C synonymous_variant 0.54
embB 4246556 p.Ala15Pro missense_variant 0.54
ethA 4326055 c.1419C>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0