TB-Profiler result

Run: SRR18002993
Summary

Run ID: SRR18002993

Sample name:

Date: 03-04-2023 19:12:55

Number of reads: 4191192

Percentage reads mapped: 97.59

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
gyrB 6579 p.Ser447Phe missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Gly missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
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 0.98
mshA 576108 p.Ala254Gly missense_variant 0.3
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 0.99
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 1472190 n.345G>A non_coding_transcript_exon_variant 0.14
rrs 1472231 n.386T>C non_coding_transcript_exon_variant 0.14
rrs 1472524 n.679G>A non_coding_transcript_exon_variant 0.2
rrs 1472732 n.887G>A non_coding_transcript_exon_variant 0.5
rrs 1472764 n.919G>A non_coding_transcript_exon_variant 0.33
rrs 1472801 n.956G>A non_coding_transcript_exon_variant 0.25
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.14
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.15
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.17
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.17
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.2
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.2
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.2
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.15
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.14
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.21
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.18
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.18
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.16
rrl 1473944 n.287G>A non_coding_transcript_exon_variant 0.13
rrl 1474300 n.643C>T non_coding_transcript_exon_variant 0.33
rrl 1474764 n.1110delA non_coding_transcript_exon_variant 0.25
rrl 1474911 n.1254G>A non_coding_transcript_exon_variant 0.17
rrl 1474925 n.1268G>A non_coding_transcript_exon_variant 0.2
rrl 1475247 n.1590G>T non_coding_transcript_exon_variant 0.25
rrl 1475337 n.1680C>T non_coding_transcript_exon_variant 0.18
rrl 1475715 n.2058G>A non_coding_transcript_exon_variant 0.14
rrl 1476174 n.2517G>A non_coding_transcript_exon_variant 0.18
rrl 1476375 n.2718C>T non_coding_transcript_exon_variant 0.14
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.14
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.13
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.11
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.11
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.12
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.13
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.12
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.12
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>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 0.98
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223010 p.Val52Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G 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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.99
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338510 c.12T>C synonymous_variant 1.0
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