TB-Profiler result

Run: SRR7796668
Summary

Run ID: SRR7796668

Sample name:

Date: 04-04-2023 20:20:50

Number of reads: 544861

Percentage reads mapped: 86.22

Strain: lineage2.2.2

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 0.99
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.89
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 0.52 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.96 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.79 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.76 isoniazid
embB 4247429 p.Met306Val missense_variant 0.79 ethambutol
ethA 4326130 c.1343delA frameshift_variant 0.92 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
gyrB 6501 p.Arg421His missense_variant 0.12
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 0.13
ccsA 620625 p.Ile245Met missense_variant 0.23
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764616 p.Asn416Ser missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778743 p.Val55Met missense_variant 0.96
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781406 c.-154_-153insC upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471730 n.-116T>C upstream_gene_variant 0.2
rrl 1474482 n.825G>T non_coding_transcript_exon_variant 0.17
rrl 1474514 n.857G>T non_coding_transcript_exon_variant 0.17
rrl 1475339 n.1682T>C non_coding_transcript_exon_variant 0.22
rrl 1475578 n.1921C>T non_coding_transcript_exon_variant 0.75
rrl 1475617 n.1960C>T non_coding_transcript_exon_variant 0.22
inhA 1673406 c.-796C>T upstream_gene_variant 0.88
rpsA 1833909 p.Asp123Ala missense_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154058 p.Gly685Val missense_variant 0.12
katG 2154253 p.Ser620Asn missense_variant 0.11
katG 2154257 p.Leu619Phe missense_variant 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
thyX 3067844 c.102G>C synonymous_variant 0.13
thyA 3074122 p.Asp117Gly missense_variant 0.85
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449606 p.Pro368Leu missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642070 p.Val179Asp missense_variant 0.11
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