TB-Profiler result

Run: SRR18002971
Summary

Run ID: SRR18002971

Sample name:

Date: 03-04-2023 19:12:09

Number of reads: 2990228

Percentage reads mapped: 87.25

Strain: lineage2.2.1

Drug-resistance: Other

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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
gyrB 6742 p.Glu501Asp missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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 0.29
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 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472890 n.1045C>T non_coding_transcript_exon_variant 0.11
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.1
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.11
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.11
rrl 1474640 n.983C>T non_coding_transcript_exon_variant 0.22
rrl 1474814 n.1157A>G non_coding_transcript_exon_variant 0.22
rrl 1475035 n.1378A>G non_coding_transcript_exon_variant 0.25
rrl 1476158 n.2501C>T non_coding_transcript_exon_variant 0.11
rrl 1476237 n.2580C>T non_coding_transcript_exon_variant 0.14
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.25
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.34
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.29
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.34
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.31
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.41
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.38
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.38
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.34
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.36
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.38
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.38
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.38
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.38
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.29
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.3
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.17
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.13
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
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 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.13
embB 4246548 p.Pro12Gln missense_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.11
embB 4246563 p.Leu17Trp missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407927 p.Glu92Asp missense_variant 1.0