TB-Profiler result

Run: SRR4034708
Summary

Run ID: SRR4034708

Sample name:

Date: 04-04-2023 06:59:46

Number of reads: 882143

Percentage reads mapped: 99.52

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 2155555 p.Gly186Val missense_variant 0.2 isoniazid
ethA 4326592 c.880_881dupTG frameshift_variant 0.12 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
gyrB 6002 p.Gly255Cys missense_variant 0.12
gyrB 6083 p.Gly282Ser missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8479 p.Gly393Asp missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760288 p.Ile161Asn missense_variant 0.12
rpoC 762866 c.-504C>T upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766175 p.Val936Ile missense_variant 0.18
rpoC 766396 c.3027G>A synonymous_variant 0.2
rpoC 766639 c.3272_3273dupAC frameshift_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.97
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800921 p.Arg38His missense_variant 0.18
fbiC 1304055 c.1125C>T synonymous_variant 0.12
fbiC 1305086 p.Trp719Leu missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472762 n.917C>T non_coding_transcript_exon_variant 0.11
rrs 1473043 n.1202delC non_coding_transcript_exon_variant 0.11
rrs 1473326 n.1481G>T non_coding_transcript_exon_variant 0.12
rrl 1475111 n.1454G>C non_coding_transcript_exon_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834739 p.Thr400Ala missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.95
PPE35 2169405 p.Asn403Ser missense_variant 0.12
PPE35 2170685 c.-73C>A upstream_gene_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289638 c.-397C>A upstream_gene_variant 0.12
eis 2714616 c.717C>T synonymous_variant 0.11
ahpC 2726010 c.-183G>A upstream_gene_variant 0.13
folC 2746499 p.Ala367Val missense_variant 0.25
Rv2752c 3064908 c.1284C>T synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449608 p.Glu369* stop_gained 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474835 p.Glu277* stop_gained 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613133 c.-17C>T upstream_gene_variant 0.15
fbiA 3641332 p.Gly264Arg missense_variant 1.0
rpoA 3878302 c.205delG frameshift_variant 0.13
clpC1 4038857 c.1848C>A synonymous_variant 0.4
clpC1 4040831 c.-127C>T upstream_gene_variant 0.14
embC 4239666 c.-197C>T upstream_gene_variant 0.15
embC 4239850 c.-13A>G upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242760 c.-473G>T upstream_gene_variant 0.18
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245823 p.Pro864Gln missense_variant 0.18
embB 4246877 p.Arg122Cys missense_variant 0.13
embB 4247969 p.Gly486Ser missense_variant 0.12
aftB 4267044 p.Thr598Ile missense_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327391 p.Pro28Gln missense_variant 0.13
whiB6 4338185 p.Ala113Ser missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0