TB-Profiler result

Run: SRR18002877
Summary

Run ID: SRR18002877

Sample name:

Date: 03-04-2023 19:07:42

Number of reads: 3145062

Percentage reads mapped: 63.68

Strain: lineage2.2.1

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 0.98
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.97
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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 7582 p.Asp94Ala missense_variant 0.93 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.93 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.98 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.93 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.97 isoniazid, ethionamide
pncA 2288835 p.Asp136Gly missense_variant 0.94 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.96 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.99
mshA 575907 p.Ala187Val missense_variant 0.99
mshA 576108 p.Ala254Gly missense_variant 0.34
ccsA 620625 p.Ile245Met missense_variant 0.97
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 764822 p.Asp485Tyr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.97
mmpL5 776182 p.Asp767Asn missense_variant 0.97
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
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.25
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.24
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.12
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.12
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.12
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.11
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.11
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.14
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.1
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.22
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.29
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.31
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.36
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.25
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.37
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.43
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.36
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.47
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.4
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.11
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.36
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.33
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.34
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.44
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.33
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.33
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.13
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.18
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834549 c.1008G>A synonymous_variant 0.97
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153929 p.Trp728Ser missense_variant 0.96
katG 2154724 p.Arg463Leu missense_variant 0.93
katG 2156121 c.-12_-11delGG upstream_gene_variant 0.99
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
ald 3086821 c.2T>C start_lost 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878567 c.-60C>G upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.99
embB 4246544 p.Thr11Pro missense_variant 0.18
embB 4246548 p.Pro12Gln missense_variant 0.19
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.19
embB 4246563 p.Leu17Trp missense_variant 0.23
embB 4246567 c.54G>T synonymous_variant 0.21
aftB 4267647 p.Asp397Gly missense_variant 0.94
ethA 4326822 p.Arg218Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.96
gid 4407927 p.Glu92Asp missense_variant 0.99