TB-Profiler result

Run: SRR19304064
Summary

Run ID: SRR19304064

Sample name:

Date: 03-04-2023 21:22:36

Number of reads: 717476

Percentage reads mapped: 13.86

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 761109 p.Asp435Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.89 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
ethA 4326718 c.754_755dupGC frameshift_variant 1.0 ethionamide, 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
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761484 p.Gly560Cys missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764611 c.1242G>T synonymous_variant 0.28
rpoC 764632 c.1263T>C synonymous_variant 0.24
rpoC 764644 c.1275G>C synonymous_variant 0.23
rpoC 764650 c.1281G>T synonymous_variant 0.19
rpoC 764668 c.1299C>T synonymous_variant 0.17
rpoC 764672 p.Gln435Glu missense_variant 0.17
rpoC 764677 c.1308C>G synonymous_variant 0.16
rpoC 764678 p.Lys437Arg missense_variant 0.16
rpoC 764686 c.1317C>T synonymous_variant 0.17
rpoC 764695 c.1326T>C synonymous_variant 0.17
rpoC 764701 c.1332C>G synonymous_variant 0.16
rpoC 764705 p.Leu446Lys missense_variant 0.16
rpoC 764716 c.1347G>C synonymous_variant 0.15
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 779440 p.Ser151Pro missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779630 c.-725T>C 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 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.15
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.15
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.14
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.14
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.14
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.14
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.2
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.33
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.56
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.64
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.64
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.64
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.62
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.64
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.64
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.64
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.66
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.66
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.68
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.68
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.75
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.72
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.71
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.69
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.55
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.31
rpsA 1833878 p.Trp113Arg missense_variant 0.11
rpsA 1834103 p.Arg188Cys missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102574 p.Gln157* stop_gained 0.11
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
folC 2746542 p.Ala353Thr missense_variant 0.11
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
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