TB-Profiler result

Run: SRR7516388
Summary

Run ID: SRR7516388

Sample name:

Date: 04-04-2023 19:27:07

Number of reads: 3044149

Percentage reads mapped: 99.67

Strain: lineage4;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 0.31
lineage4 Euro-American LAM;T;S;X;H None 0.69
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.3
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.33
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 0.31 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.35 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.24 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asn missense_variant 0.65 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.31 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.68 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.4 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289009 p.Gly78Asp missense_variant 0.35 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.26 kanamycin
embB 4247429 p.Met306Val missense_variant 0.64 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.28 ethambutol
ethA 4326770 c.703delT frameshift_variant 0.32 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 7892 c.591G>A synonymous_variant 0.69
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.33
mshA 575907 p.Ala187Val missense_variant 0.28
mshA 576108 p.Ala254Gly missense_variant 0.24
ccsA 620619 c.729G>A synonymous_variant 0.73
ccsA 620625 p.Ile245Met missense_variant 0.29
rpoB 762011 c.2205G>A synonymous_variant 0.32
rpoB 762312 p.Gly836Ser missense_variant 0.31
rpoC 763031 c.-339T>C upstream_gene_variant 0.36
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.3
mmpL5 776182 p.Asp767Asn missense_variant 0.26
mmpL5 778090 p.Gly131Arg missense_variant 0.76
mmpS5 779615 c.-710C>G upstream_gene_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304610 c.1680C>T synonymous_variant 0.67
Rv1258c 1406760 c.580_581insC frameshift_variant 0.31
embR 1416966 p.Ala128Pro missense_variant 0.63
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474074 n.417C>T non_coding_transcript_exon_variant 0.68
rpsA 1834177 c.636A>C synonymous_variant 0.31
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102417 p.Ala209Val missense_variant 0.35
katG 2154594 c.1518G>A synonymous_variant 0.69
katG 2154724 p.Arg463Leu missense_variant 0.3
PPE35 2167926 p.Leu896Ser missense_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064810 p.Thr461Ile missense_variant 0.61
ald 3086731 c.-89A>G upstream_gene_variant 0.42
ald 3086788 c.-32T>C upstream_gene_variant 0.44
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568819 c.-140C>G upstream_gene_variant 0.71
Rv3236c 3612813 p.Thr102Ala missense_variant 0.34
rpoA 3878575 c.-68C>T upstream_gene_variant 0.64
clpC1 4038318 p.Pro796Leu missense_variant 0.62
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242835 c.-398C>T upstream_gene_variant 0.76
embA 4243346 c.114A>G synonymous_variant 0.32
embA 4243460 c.228C>T synonymous_variant 0.26
embB 4246584 p.Arg24Pro missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 0.28
ethA 4327310 p.Ser55Cys missense_variant 0.63
whiB6 4338371 p.Thr51Pro missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.29
gid 4407927 p.Glu92Asp missense_variant 0.4