TB-Profiler result

Run: SRR1165236
Summary

Run ID: SRR1165236

Sample name:

Date: 02-04-2023 23:47:56

Number of reads: 2287012

Percentage reads mapped: 52.16

Strain: lineage2.2

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
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 7570 p.Ala90Val missense_variant 0.68 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.97 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.92 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.84 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288724 c.517dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
alr 3841083 p.Leu113Arg missense_variant 1.0 cycloserine
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
gid 4407967 p.Leu79Ser missense_variant 1.0 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 7581 p.Asp94Ser missense_variant 0.19
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
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
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.12
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.33
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.34
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.34
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.33
rrs 1472129 n.284G>T non_coding_transcript_exon_variant 0.34
rrs 1472135 n.290C>G non_coding_transcript_exon_variant 0.35
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.35
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.35
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.34
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.33
rrs 1472153 n.308G>C non_coding_transcript_exon_variant 0.34
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.38
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.1
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.17
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.17
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.22
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.25
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.56
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.61
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.64
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.7
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.63
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.16
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.14
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.14
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.25
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.28
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.38
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.38
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.42
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.41
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.41
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.39
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.4
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.51
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.54
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.58
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.59
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.59
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.59
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.6
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.58
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.59
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.57
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.59
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.75
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.76
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.76
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.71
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.7
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.66
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.67
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.62
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.62
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.21
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 0.97
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859623 p.Pro266Ala missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612286 c.830dupG frameshift_variant 0.2
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