TB-Profiler result

Run: ERR5866376
Summary

Run ID: ERR5866376

Sample name:

Date: 02-04-2023 00:39:16

Number of reads: 895853

Percentage reads mapped: 97.27

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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.Asp94Gly missense_variant 0.26 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.89 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embB 4247730 p.Gly406Ala missense_variant 1.0 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 7290 c.-12A>G upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8046 p.Gly249Ser missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575889 p.Ala181Asp missense_variant 0.22
mshA 575907 p.Ala187Val missense_variant 0.82
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620757 c.867C>T synonymous_variant 0.13
rpoB 759711 c.-95_-88delGCCGAAAC upstream_gene_variant 0.2
rpoB 759723 c.-84C>T upstream_gene_variant 0.2
rpoB 759726 c.-81A>T upstream_gene_variant 0.2
rpoB 759727 c.-80A>T upstream_gene_variant 0.2
rpoB 759730 c.-77A>G upstream_gene_variant 0.2
rpoB 759733 c.-74_-73insGTTTCGGC upstream_gene_variant 0.2
rpoB 760688 p.Phe294Leu missense_variant 0.14
rpoB 761184 p.Glu460Lys missense_variant 0.12
rpoC 762962 c.-408C>A upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763630 c.261G>C synonymous_variant 0.11
rpoC 766334 p.Val989Ile missense_variant 0.11
rpoC 767273 p.Gly1302Cys missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.87
mmpL5 777170 c.1311T>C synonymous_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 0.89
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474469 n.812T>A non_coding_transcript_exon_variant 0.12
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.11
rrl 1476294 n.2642delC non_coding_transcript_exon_variant 0.2
inhA 1674162 c.-40C>T upstream_gene_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918003 p.Gln22Lys missense_variant 0.15
tlyA 1918018 p.Ile27Val missense_variant 1.0
ndh 2101919 p.Arg375Met missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155789 p.His108Arg missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 0.96
Rv1979c 2223180 c.-16A>G upstream_gene_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289071 p.His57Gln missense_variant 1.0
kasA 2519267 p.Val385Ile missense_variant 0.12
eis 2715332 p.Val1Leu missense_variant 1.0
pepQ 2859417 c.1002C>A synonymous_variant 0.11
Rv2752c 3064940 c.1251delA frameshift_variant 0.14
Rv2752c 3065518 p.Leu225Pro missense_variant 1.0
Rv2752c 3066146 c.45delG frameshift_variant 0.12
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612288 p.Gly277Arg missense_variant 0.18
Rv3236c 3612805 c.311delG frameshift_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642018 c.485_489delATGCC frameshift_variant 0.18
fbiB 3642027 c.494delT frameshift_variant 0.18
fbiB 3642031 p.Gly166Ala missense_variant 0.18
fbiB 3642033 c.499_500insA frameshift_variant 0.18
fbiB 3642037 c.503_504insGGCAT frameshift_variant 0.18
fbiB 3642563 p.Asp343Glu missense_variant 0.25
rpoA 3877969 p.Ala180Gly missense_variant 0.96
clpC1 4039162 p.His515Asp missense_variant 0.1
embA 4242325 c.-908C>A upstream_gene_variant 0.5
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
embA 4243641 c.414_415dupGC frameshift_variant 0.13
embA 4243835 c.603G>A synonymous_variant 0.11
embA 4245997 p.Trp922Ser missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269941 c.-108C>A upstream_gene_variant 0.15
ubiA 4270026 c.-193C>G upstream_gene_variant 0.2
ethA 4326049 c.1425C>T synonymous_variant 0.13
ethA 4326155 p.Leu440Pro missense_variant 1.0
ethR 4327060 c.-489G>A upstream_gene_variant 0.11
ethR 4327940 p.Ser131Thr missense_variant 0.1
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