TB-Profiler result

Run: SRR10869254
Summary

Run ID: SRR10869254

Sample name:

Date: 02-04-2023 19:45:47

Number of reads: 2391873

Percentage reads mapped: 90.65

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
gyrA 7582 p.Asp94Gly missense_variant 0.65 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.14 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.99 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 0.36
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 0.98
rpoC 764931 p.Ala521Asp missense_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 1472558 n.713G>A non_coding_transcript_exon_variant 0.14
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.14
rrs 1472571 n.726G>A non_coding_transcript_exon_variant 0.15
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.17
rrs 1472606 n.761C>G non_coding_transcript_exon_variant 0.21
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.22
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.23
rrs 1472645 n.800G>C non_coding_transcript_exon_variant 0.22
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.16
rrs 1472660 n.815T>A non_coding_transcript_exon_variant 0.17
rrs 1472666 n.821G>T non_coding_transcript_exon_variant 0.16
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.12
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.12
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.12
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.12
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.12
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.13
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.17
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.16
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.16
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.16
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.15
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.15
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.15
rrs 1472993 n.1148G>T non_coding_transcript_exon_variant 0.16
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.19
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.13
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.13
rrs 1473134 n.1289T>C non_coding_transcript_exon_variant 0.11
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.13
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.11
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.13
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.13
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.13
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.13
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.13
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.15
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.15
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.14
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.14
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.16
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.17
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.24
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.21
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.21
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.22
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.22
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.25
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.19
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.19
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.21
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.18
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.14
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.12
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.14
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.14
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.19
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.21
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.23
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.23
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.23
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.18
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.17
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.17
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.17
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.17
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.17
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.17
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.19
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.21
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.18
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.17
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
PPE35 2170065 p.Ala183Gly missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.54
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 4246584 p.Arg24Pro missense_variant 0.27
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