TB-Profiler result

Run: SRR9971035
Summary

Run ID: SRR9971035

Sample name:

Date: 04-04-2023 23:07:52

Number of reads: 6616818

Percentage reads mapped: 99.22

Strain: lineage2.2.1

Drug-resistance: RR-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 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
rpoB 761139 p.His445Asp missense_variant 0.13 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.83 rifampicin
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 1.0
mshA 576108 p.Ala254Gly missense_variant 0.28
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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 1472717 n.872C>A non_coding_transcript_exon_variant 0.15
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.27
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.27
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.17
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.33
rrl 1474797 n.1140G>A non_coding_transcript_exon_variant 0.14
rrl 1474801 n.1144G>A non_coding_transcript_exon_variant 0.27
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.33
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.33
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.33
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.33
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.33
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.36
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 0.29
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.29
rrl 1474911 n.1254G>A non_coding_transcript_exon_variant 0.18
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.27
rrl 1474933 n.1276A>G non_coding_transcript_exon_variant 0.29
rrl 1474934 n.1277C>T non_coding_transcript_exon_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_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
thyA 3073840 p.Asn211Ile missense_variant 0.99
thyA 3073842 p.Asp210Glu 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 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.38
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0