TB-Profiler result

Run: SRR5266539
Summary

Run ID: SRR5266539

Sample name:

Date: 04-04-2023 10:00:38

Number of reads: 758834

Percentage reads mapped: 97.25

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 6750 p.Ala504Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289222 p.Val7Ala missense_variant 1.0 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326705 c.768delG 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
gyrB 5788 c.549G>T synonymous_variant 0.13
gyrA 6808 c.-494C>T upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8143 p.Asp281Val missense_variant 0.12
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
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766763 p.Ile1132Leu 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 1.0
mmpL5 777866 p.Gln205His missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303053 c.123G>T synonymous_variant 0.13
fbiC 1303225 c.298delG frameshift_variant 0.15
fbiC 1305271 p.Ile781Val missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416944 p.Ser135Asn missense_variant 0.12
embR 1417270 c.78C>A synonymous_variant 0.11
atpE 1460873 c.-172G>A upstream_gene_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473513 n.-145T>C upstream_gene_variant 0.14
rrl 1473531 n.-127T>C upstream_gene_variant 0.11
fabG1 1673279 c.-160delC upstream_gene_variant 0.11
inhA 1674840 c.639C>T synonymous_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102494 c.549T>C synonymous_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154912 p.His400Gln missense_variant 0.11
katG 2156130 c.-19A>G upstream_gene_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168915 c.1698G>A synonymous_variant 0.29
Rv1979c 2221743 c.1422T>C synonymous_variant 0.2
Rv1979c 2222124 p.Asp347Glu missense_variant 0.14
Rv1979c 2223226 c.-62A>G upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860114 c.304delG frameshift_variant 0.11
thyX 3067206 p.Ala247Gly missense_variant 0.13
thyA 3073750 p.Tyr241Phe missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087236 c.417A>C synonymous_variant 1.0
fbiD 3339504 p.Ile129Met missense_variant 0.91
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840621 p.Gly267Asp missense_variant 0.11
clpC1 4040755 c.-51A>T upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246794 p.Ala94Val missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4270002 c.-169G>T upstream_gene_variant 0.13
ethA 4326454 c.1020C>T synonymous_variant 0.17
whiB6 4338563 c.-42G>T upstream_gene_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