TB-Profiler result

Run: SRR3675272
Summary

Run ID: SRR3675272

Sample name:

Date: 04-04-2023 05:25:03

Number of reads: 288736

Percentage reads mapped: 98.88

Strain: lineage3

Drug-resistance: HR-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
katG 2155573 p.Thr180Lys missense_variant 0.14 isoniazid
ahpC 2726145 c.-48G>T upstream_gene_variant 0.17 isoniazid
ethA 4327132 c.341dupA frameshift_variant 0.29 ethionamide, ethionamide
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 8667 p.Ala456Ser missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.25
fgd1 491057 p.Thr92Ile missense_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.33
ccsA 620537 p.Val216Gly missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.25
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761592 c.1788delC frameshift_variant 0.25
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764566 c.1197C>A synonymous_variant 0.22
rpoC 765538 p.Trp723Cys missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777158 c.1323C>A synonymous_variant 0.18
mmpR5 778016 c.-974G>T upstream_gene_variant 0.22
mmpL5 778537 c.-57G>A upstream_gene_variant 1.0
mmpL5 778570 c.-90C>A upstream_gene_variant 0.2
mmpS5 778872 p.Leu12Met missense_variant 0.18
mmpS5 779680 c.-775G>T upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473666 n.9G>A non_coding_transcript_exon_variant 1.0
rrl 1473774 n.117G>A non_coding_transcript_exon_variant 0.12
rrl 1474319 n.662C>A non_coding_transcript_exon_variant 0.17
rrl 1475008 n.1351C>A non_coding_transcript_exon_variant 0.95
ndh 2103221 c.-179C>T upstream_gene_variant 1.0
katG 2154051 c.2061G>T synonymous_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155007 p.Gly369Ser missense_variant 0.22
katG 2156289 c.-178G>A upstream_gene_variant 0.2
PPE35 2167865 c.2748G>C synonymous_variant 0.2
PPE35 2167868 c.2745A>C synonymous_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.15
PPE35 2169910 p.Asn235Tyr missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.39
PPE35 2170053 p.Thr187Ser missense_variant 0.47
Rv1979c 2221884 c.1281G>T 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 2289783 c.-542G>T upstream_gene_variant 0.29
eis 2715172 p.Pro54Gln missense_variant 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3064917 p.Asn425Lys missense_variant 0.18
Rv2752c 3065791 p.Thr134Ile missense_variant 0.25
thyA 3074531 c.-60G>T upstream_gene_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448397 c.-107G>A upstream_gene_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840975 p.Gly149Asp missense_variant 0.22
ddn 3986840 c.-4C>A upstream_gene_variant 0.4
panD 4044109 p.Tyr58Phe missense_variant 0.29
embC 4240648 c.786C>T synonymous_variant 0.29
embC 4241424 p.Arg521Leu missense_variant 0.33
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245320 c.2088C>A synonymous_variant 0.25
embA 4245372 p.Pro714Ser missense_variant 1.0
embB 4247652 p.Ser380Ile missense_variant 0.15
embB 4249456 c.2943G>A synonymous_variant 1.0
aftB 4268390 c.447G>T synonymous_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0