TB-Profiler result

Run: SRR16088264
Summary

Run ID: SRR16088264

Sample name:

Date: 03-04-2023 16:05:33

Number of reads: 2206238

Percentage reads mapped: 99.63

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 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
gyrB 6579 p.Ser447Phe missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289150 p.Ile31Ser missense_variant 1.0 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4327132 c.341delA frameshift_variant 1.0 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
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 1.0
mshA 576446 p.Thr367Pro missense_variant 0.22
mshA 576456 p.Val370Gly missense_variant 0.4
mshA 576489 p.Val381Gly missense_variant 0.25
mshA 576616 c.1269G>C synonymous_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.25
rpoC 764715 p.Leu449Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.16
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
fabG1 1673553 p.Asp38Glu missense_variant 0.35
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
PPE35 2170065 p.Ala183Gly missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.27
eis 2715294 p.Trp13* stop_gained 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.24
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3064823 p.Val457Leu missense_variant 0.17
Rv2752c 3065126 p.Ser356Pro missense_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087816 p.Cys333Gly missense_variant 0.18
fbiD 3339734 p.Ala206Gly missense_variant 0.86
fbiD 3339749 p.Val211Ala missense_variant 0.67
fbiD 3339751 p.Ala212Pro missense_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.71
whiB7 3568431 c.249C>G synonymous_variant 0.38
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878590 c.-83G>T upstream_gene_variant 0.5
rpoA 3878597 c.-90G>C upstream_gene_variant 1.0
rpoA 3878637 c.-130G>C upstream_gene_variant 0.67
rpoA 3878641 c.-134C>G upstream_gene_variant 0.79
embC 4240409 p.Pro183Ala missense_variant 0.36
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.24
embB 4248328 c.1815G>C synonymous_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338200 p.Asp108His missense_variant 0.14
whiB6 4338371 p.Thr51Pro 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