TB-Profiler result

Run: SRR11972447
Summary

Run ID: SRR11972447

Sample name:

Date: 03-04-2023 05:42:42

Number of reads: 1189072

Percentage reads mapped: 97.34

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 0.99
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 7581 p.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asn missense_variant 0.94 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288697 p.Leu182Ser missense_variant 0.12 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.97 ethambutol
embB 4248003 p.Gln497Arg 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 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761827 p.His674Arg 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
mmpR5 779121 c.138_139dupTG frameshift_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 1472580 n.735C>T non_coding_transcript_exon_variant 0.11
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.15
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.12
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.13
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.15
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.19
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.19
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.23
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.17
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.16
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.16
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.14
rrs 1473129 n.1284C>T non_coding_transcript_exon_variant 0.11
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.1
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.1
rrl 1475060 n.1404delC non_coding_transcript_exon_variant 0.17
rrl 1475063 n.1406A>T non_coding_transcript_exon_variant 0.15
rrl 1475065 n.1408G>A non_coding_transcript_exon_variant 0.15
rrl 1475067 n.1410A>G non_coding_transcript_exon_variant 0.15
rrl 1475076 n.1419C>A non_coding_transcript_exon_variant 0.15
rrl 1475079 n.1422T>C non_coding_transcript_exon_variant 0.13
rrl 1475081 n.1424C>T non_coding_transcript_exon_variant 0.13
rrl 1475090 n.1433A>T non_coding_transcript_exon_variant 0.12
rrl 1475093 n.1436C>T non_coding_transcript_exon_variant 0.12
rrl 1475108 n.1451C>T non_coding_transcript_exon_variant 0.11
rrl 1475111 n.1454G>A non_coding_transcript_exon_variant 0.11
rrl 1475116 n.1459G>A non_coding_transcript_exon_variant 0.11
rrl 1475119 n.1462C>T non_coding_transcript_exon_variant 0.11
rrl 1475696 n.2039T>A non_coding_transcript_exon_variant 0.12
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.12
rrl 1475703 n.2046A>T non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 0.95
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
PPE35 2170048 p.Leu189Val missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289193 p.Gly17Cys missense_variant 1.0
Rv2752c 3067039 c.-848T>C 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
rpoA 3877983 c.525C>A synonymous_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4245794 c.-720G>T upstream_gene_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326818 p.Asp219Ala missense_variant 0.95
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