TB-Profiler result

Run: SRR18003040
Summary

Run ID: SRR18003040

Sample name:

Date: 03-04-2023 19:15:19

Number of reads: 1890006

Percentage reads mapped: 34.4

Strain: lineage2.2.1

Drug-resistance: MDR-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
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.14 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289097 p.Asp49Asn missense_variant 1.0 pyrazinamide
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
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Ala 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 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 1472655 n.810G>T non_coding_transcript_exon_variant 0.12
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.13
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.11
rrs 1472674 n.829T>G non_coding_transcript_exon_variant 0.11
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.11
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.12
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.14
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.16
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.1
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.14
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.17
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.13
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.15
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.15
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.12
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.13
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.12
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.16
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.14
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.18
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.15
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.11
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.1
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.11
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.12
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.15
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.15
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.11
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.22
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.3
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.21
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.18
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.35
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.3
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.16
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.35
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.34
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.36
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.19
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.33
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.19
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.29
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.17
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.32
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.16
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.35
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.34
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.14
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.23
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.39
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.31
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.34
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.14
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.23
rrl 1476512 n.2855C>T 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
PPE35 2168117 c.2496C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726453 c.261T>C synonymous_variant 0.11
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
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