TB-Profiler result

Run: SRR5709797
Summary

Run ID: SRR5709797

Sample name:

Date: 04-04-2023 10:58:35

Number of reads: 1338795

Percentage reads mapped: 99.46

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 0.88
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.93
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.9
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 7581 p.Asp94His missense_variant 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761131 p.Gly442Glu missense_variant 0.16 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.81 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.87 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247469 p.Tyr319Ser missense_variant 0.93 ethambutol
ethA 4326833 c.639_640delGT frameshift_variant 0.94 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 0.98
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.11
gyrA 9143 c.1842T>C synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.97
ccsA 620625 p.Ile245Met missense_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.16
rpoC 763886 c.517C>A synonymous_variant 0.17
rpoC 764616 p.Asn416Ser missense_variant 0.95
rpoC 765171 p.Pro601Leu missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.92
mmpS5 779615 c.-710C>G upstream_gene_variant 0.88
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303312 p.Ile128Val missense_variant 0.82
Rv1258c 1406760 c.580_581insC frameshift_variant 0.89
atpE 1461227 c.183G>A synonymous_variant 0.28
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 0.89
rpsA 1834319 p.Val260Ile missense_variant 0.12
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 2167983 p.Gly877Asp missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.16
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.97
clpC1 4040517 p.Val63Ala missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.91
embA 4243848 p.Val206Met missense_variant 0.16
embA 4244096 c.864C>T synonymous_variant 0.16
aftB 4267647 p.Asp397Gly missense_variant 0.85
ubiA 4269718 p.Ala39Gly missense_variant 0.95
ethA 4327483 c.-10G>A upstream_gene_variant 0.14
whiB6 4338242 p.Gln94Glu missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.14
gid 4407927 p.Glu92Asp missense_variant 0.93