TB-Profiler result

Run: SRR5149238
Summary

Run ID: SRR5149238

Sample name:

Date: 04-04-2023 09:09:35

Number of reads: 494471

Percentage reads mapped: 92.3

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 0.92
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.92
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.84
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 6737 p.Thr500Pro missense_variant 0.9 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.67 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.91 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.93 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.11 isoniazid, ethionamide
ahpC 2726145 c.-48G>A upstream_gene_variant 0.54 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.89 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 7892 c.591G>A synonymous_variant 0.25
gyrA 8452 p.Ala384Val missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 0.94
rpoB 759615 c.-192A>C upstream_gene_variant 0.27
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767123 p.Val1252Met missense_variant 0.92
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775694 p.Ile929Met missense_variant 0.92
mmpL5 776100 p.Thr794Ile missense_variant 0.83
mmpL5 776182 p.Asp767Asn missense_variant 0.33
mmpL5 777160 p.Ala441Ser missense_variant 0.15
mmpL5 777390 p.Phe364Cys missense_variant 0.15
mmpL5 778447 c.24_33dupGCCGACGGGC frameshift_variant 0.33
mmpR5 779130 c.144dupC frameshift_variant 0.67
mmpS5 779615 c.-710C>G upstream_gene_variant 0.9
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800802 c.-7C>T upstream_gene_variant 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 0.82
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472012 n.167A>G non_coding_transcript_exon_variant 0.13
rrl 1474961 n.1304T>G non_coding_transcript_exon_variant 0.33
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.27
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.27
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.25
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.27
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.13
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.14
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.15
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.14
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 0.87
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102578 p.Phe155Leu missense_variant 0.18
katG 2154086 p.Gly676Arg missense_variant 1.0
katG 2154217 p.Arg632His missense_variant 0.85
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155935 c.177T>G synonymous_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 0.91
PPE35 2168711 c.1902A>G synonymous_variant 0.17
Rv1979c 2222042 p.Thr375Pro missense_variant 0.22
Rv1979c 2222532 c.633C>A synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289028 p.Cys72Gly missense_variant 0.87
pncA 2289786 c.-545G>T upstream_gene_variant 0.13
ribD 2987259 p.Leu141Val missense_variant 0.67
Rv2752c 3065129 c.1063C>T synonymous_variant 0.92
ald 3086788 c.-32T>C upstream_gene_variant 0.94
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568594 p.Phe29Cys missense_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612971 p.Leu49Trp missense_variant 0.29
fbiB 3640647 c.-888G>T upstream_gene_variant 0.25
embC 4240026 p.Thr55Asn missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248004 p.Gln497His missense_variant 0.71
embB 4248005 p.Thr498Ser missense_variant 0.71
embB 4249305 p.Asn931Thr missense_variant 0.29
aftB 4266974 c.1863C>A synonymous_variant 0.2
aftB 4267190 c.1647T>G synonymous_variant 0.2
aftB 4267240 p.Phe533Val missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 0.8
ethA 4326617 p.Tyr286Ser missense_variant 0.18
ethR 4326658 c.-891T>G upstream_gene_variant 0.33
ethA 4326676 p.Ser266Arg missense_variant 0.73
ethR 4327688 p.Val47Gly missense_variant 0.15
ethR 4327695 p.Asp49Glu missense_variant 0.15
ethR 4327697 p.Leu50Arg missense_variant 0.17
whiB6 4338326 p.Ala66Thr missense_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.7
gid 4407927 p.Glu92Asp missense_variant 0.89