TB-Profiler result

Run: SRR12882160

Summary

Run ID: SRR12882160

Sample name:

Date: 03-04-2023 07:14:20

Number of reads: 1345699

Percentage reads mapped: 96.77

Strain: lineage3

Drug-resistance: MDR-TB


Download CSV Download TXT Download PDF Download JSON
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 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 2288746 c.495delC frameshift_variant 1.0 pyrazinamide, 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 6554 p.Pro439Thr missense_variant 0.22
gyrA 6766 c.-536G>T upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8765 p.Asp488Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761010 p.Asp402Tyr missense_variant 0.2
rpoB 761170 p.Gly455Asp missense_variant 0.15
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763583 p.Gly72Cys missense_variant 0.2
rpoC 764181 p.Asp271Gly missense_variant 1.0
rpoC 764918 p.Val517Leu missense_variant 1.0
rpoC 767294 p.Asp1309Tyr missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778170 p.Ala104Asp missense_variant 0.17
mmpS5 778484 p.Ser141Tyr missense_variant 0.18
mmpS5 778813 p.Phe31Leu missense_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416523 c.825G>T synonymous_variant 0.18
atpE 1461036 c.-9G>T upstream_gene_variant 0.25
atpE 1461089 c.45G>T synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.5
fabG1 1673782 p.Gly115Arg missense_variant 0.29
rpsA 1833384 c.-158C>A upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102997 c.46C>A synonymous_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2168592 p.Pro674Gln missense_variant 0.18
PPE35 2170769 c.-157C>T upstream_gene_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
pncA 2289395 c.-154C>A upstream_gene_variant 0.25
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726117 c.-76T>A upstream_gene_variant 1.0
thyA 3074436 c.36C>A synonymous_variant 0.2
thyA 3074448 c.24G>A synonymous_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087227 c.408C>A synonymous_variant 0.18
ald 3087399 p.Val194Ile missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038248 c.2457C>T synonymous_variant 1.0
embC 4241870 p.Val670Met missense_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.1
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4246563 p.Leu17Trp missense_variant 0.12
embB 4249210 c.2697G>T synonymous_variant 0.18
aftB 4268879 c.-43G>T upstream_gene_variant 0.15
aftB 4269519 c.-683G>T upstream_gene_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0