TB-Profiler result

Run: SRR1173632
Summary

Run ID: SRR1173632

Sample name:

Date: 03-04-2023 03:28:54

Number of reads: 517097

Percentage reads mapped: 72.11

Strain: lineage2.2.1

Drug-resistance: RR-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 0.99
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 1.0 rifampicin
embB 4247431 p.Met306Ile missense_variant 0.19 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 8930 c.1629C>T synonymous_variant 0.11
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 764665 c.1296C>G synonymous_variant 0.22
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 779410 p.Asp141His 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 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.1
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.1
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.1
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 1476336 n.2679C>T non_coding_transcript_exon_variant 0.2
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.2
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.26
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.26
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.26
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.26
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.25
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.24
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.24
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.24
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.23
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.29
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.3
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.29
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.31
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.2
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.2
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
katG 2156230 c.-119C>A upstream_gene_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289268 c.-27G>C upstream_gene_variant 1.0
eis 2715188 p.Arg49Cys missense_variant 0.82
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
fbiB 3640647 c.-888G>A upstream_gene_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 4338250 p.Ala91Glu missense_variant 0.85
whiB6 4338346 p.Arg59Pro missense_variant 0.15
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