TB-Profiler result

Run: SRR10869051
Summary

Run ID: SRR10869051

Sample name:

Date: 02-04-2023 19:37:35

Number of reads: 2656010

Percentage reads mapped: 95.83

Strain: lineage2.2.1

Drug-resistance: HR-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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
ethR 4327831 p.Ala95Thr missense_variant 1.0 ethionamide
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 0.31
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_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 778979 c.-74G>T upstream_gene_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 1472127 n.282C>T non_coding_transcript_exon_variant 0.14
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.14
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.14
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.15
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.15
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.14
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.14
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.12
rrl 1475751 n.2094C>G non_coding_transcript_exon_variant 0.12
rrl 1475752 n.2095C>G non_coding_transcript_exon_variant 0.12
rrl 1475753 n.2096C>A non_coding_transcript_exon_variant 0.12
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.12
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.12
rrl 1475776 n.2119G>C non_coding_transcript_exon_variant 0.12
rrl 1475777 n.2120A>C non_coding_transcript_exon_variant 0.12
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.12
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.13
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.13
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.13
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.13
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.15
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.13
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.15
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.15
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.16
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.12
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.12
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.12
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.12
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.12
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.13
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.13
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.12
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.13
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.15
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.2
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.23
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.29
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.29
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.29
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.29
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.28
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.22
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.21
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.21
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.21
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.2
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.21
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.2
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.21
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.21
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.21
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.31
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.34
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.35
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.36
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.32
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.32
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.32
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.3
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.3
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.29
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.24
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.18
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.13
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
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 4246542 p.Ser10Asn missense_variant 0.17
embB 4246584 p.Arg24Pro missense_variant 0.2
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 4407927 p.Glu92Asp missense_variant 1.0