TB-Profiler result

Run: SRR15600376
Summary

Run ID: SRR15600376

Sample name:

Date: 03-04-2023 14:18:05

Number of reads: 8422593

Percentage reads mapped: 92.11

Strain: lineage2.2.1.1

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 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
gyrA 7570 p.Ala90Val missense_variant 0.96 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.15 streptomycin
katG 2155699 p.Asn138Ser missense_variant 0.98 isoniazid
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.93
mshA 576108 p.Ala254Gly missense_variant 0.23
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763028 c.-342T>C upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763034 c.-336C>G upstream_gene_variant 0.14
rpoC 763040 c.-330C>G upstream_gene_variant 0.16
rpoC 763070 c.-300T>C upstream_gene_variant 0.14
rpoC 763085 c.-285C>G upstream_gene_variant 0.17
rpoC 763115 c.-255T>C upstream_gene_variant 0.14
rpoC 763528 c.159G>A synonymous_variant 0.14
rpoC 763546 c.177A>G synonymous_variant 0.15
rpoC 763594 c.225C>T synonymous_variant 0.12
rpoC 764353 c.984G>C synonymous_variant 0.17
rpoC 764365 c.996C>T synonymous_variant 0.13
rpoC 765753 p.Asp795Ala missense_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 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.16
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.19
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.22
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.22
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.15
rrl 1473945 n.288T>A non_coding_transcript_exon_variant 0.14
rrl 1473946 n.289A>T non_coding_transcript_exon_variant 0.14
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.15
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.14
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.15
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.15
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.25
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.16
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.17
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.16
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.21
rrl 1475013 n.1356G>A non_coding_transcript_exon_variant 0.22
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.25
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.23
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.14
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.15
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.15
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.14
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.15
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.16
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.18
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.23
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.22
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.18
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.18
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.19
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.15
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.18
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.19
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.17
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.17
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.16
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.16
rpsA 1833940 c.399C>G synonymous_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154469 p.Gly548Ala missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_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
rpoA 3877818 c.690A>G synonymous_variant 0.15
rpoA 3878364 c.144A>T synonymous_variant 0.14
rpoA 3878367 c.141C>G synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245131 c.1899G>A synonymous_variant 0.94
embB 4246584 p.Arg24Pro missense_variant 0.3
embB 4248115 c.1602C>T synonymous_variant 0.9
embB 4248304 c.1791G>C synonymous_variant 0.15
embB 4248316 c.1803C>G synonymous_variant 0.15
embB 4248319 c.1806A>G synonymous_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 0.99
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