TB-Profiler result

Run: SRR7131125
Summary

Run ID: SRR7131125

Sample name:

Date: 04-04-2023 18:46:12

Number of reads: 1818845

Percentage reads mapped: 99.99

Strain: lineage2.2.1

Drug-resistance: Other

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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
rrs 1472272 n.427G>T non_coding_transcript_exon_variant 0.11 streptomycin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.15 streptomycin
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
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779209 p.Leu74Val 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 1472274 n.429A>G non_coding_transcript_exon_variant 0.11
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.18
rrs 1472496 n.651T>G non_coding_transcript_exon_variant 0.18
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.17
rrs 1472504 n.659A>T non_coding_transcript_exon_variant 0.17
rrs 1472508 n.663T>C non_coding_transcript_exon_variant 0.2
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.14
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.13
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.17
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.15
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.17
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.18
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.18
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.18
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.15
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 0.15
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.15
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.15
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.15
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.15
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.18
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.19
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.19
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.29
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.2
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.29
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.19
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.19
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.19
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.2
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.2
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.17
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.19
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.16
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
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326676 p.Ser266Arg missense_variant 1.0
ethA 4326977 p.His166Arg 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