TB-Profiler result

Run: ERR2515657
Summary

Run ID: ERR2515657

Sample name:

Date: 31-03-2023 21:02:54

Number of reads: 293330

Percentage reads mapped: 99.67

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
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
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 6362 c.-940T>C upstream_gene_variant 0.11
gyrA 7075 c.-227T>C upstream_gene_variant 0.14
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 490700 c.-83G>A upstream_gene_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575244 c.-104C>T upstream_gene_variant 0.13
mshA 575646 p.Val100Glu missense_variant 0.15
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764987 p.Gln540* stop_gained 0.15
rpoC 765254 p.Val629Met missense_variant 0.11
rpoC 766719 p.Asp1117Gly missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776565 p.Pro639Leu missense_variant 0.12
mmpL5 776644 p.Met613Val missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 0.89
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302944 c.15delA frameshift_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471799 n.-47A>T upstream_gene_variant 0.2
rrs 1473048 n.1205_1206delAT non_coding_transcript_exon_variant 0.12
rrl 1474255 n.598C>G non_coding_transcript_exon_variant 0.17
rrl 1474599 n.942T>A non_coding_transcript_exon_variant 0.17
rrl 1476504 n.2847T>C non_coding_transcript_exon_variant 0.12
inhA 1673742 c.-460C>T upstream_gene_variant 0.17
inhA 1674736 c.537delC frameshift_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917907 c.-33C>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918105 p.Thr56Ser missense_variant 0.11
ndh 2102163 p.Arg294Trp missense_variant 0.13
ndh 2102590 c.453A>T synonymous_variant 0.13
ndh 2103200 c.-158C>G upstream_gene_variant 0.12
ndh 2103226 c.-184C>G upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169408 p.Phe402Cys missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518269 p.Thr52Asn missense_variant 0.1
ahpC 2726415 p.Phe75Leu missense_variant 0.13
ribD 2986914 p.Gly26Ser missense_variant 0.33
Rv2752c 3065336 p.Leu286Ile missense_variant 0.12
Rv2752c 3066372 c.-181G>A upstream_gene_variant 0.13
ald 3086739 c.-81G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640515 c.-28T>A upstream_gene_variant 0.13
fbiA 3640717 p.Cys59Arg missense_variant 0.12
fbiB 3641944 p.Arg137His missense_variant 0.14
rpoA 3877638 c.870T>A synonymous_variant 0.13
rpoA 3878002 p.Ser169Leu missense_variant 0.14
clpC1 4038461 c.2244G>T synonymous_variant 0.13
embC 4241177 p.Gly439Trp missense_variant 0.12
embC 4241481 c.1621delG frameshift_variant 0.13
embC 4241696 p.Ala612Ser missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242745 c.-488A>G upstream_gene_variant 0.14
embC 4243032 p.Trp1057Leu missense_variant 0.11
embA 4243286 c.54C>A synonymous_variant 0.14
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246308 p.Thr1026Ala missense_variant 0.17
embB 4246548 p.Pro12Leu missense_variant 0.15
embB 4246900 c.387C>T synonymous_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326782 p.Glu231Gly missense_variant 0.11
whiB6 4338216 p.Asn102Lys missense_variant 0.15
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