TB-Profiler result

Run: ERR5864540
Summary

Run ID: ERR5864540

Sample name:

Date: 01-04-2023 23:25:13

Number of reads: 1270936

Percentage reads mapped: 99.41

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
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
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
ccsA 619889 c.-2G>A upstream_gene_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762126 p.Val774Met missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 766520 p.Gly1051Ser missense_variant 0.11
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775744 p.Gly913Ser missense_variant 0.14
mmpL5 775852 p.Ser877Gly missense_variant 0.1
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801029 p.Gly74Asp missense_variant 0.11
fbiC 1304001 c.1071C>T synonymous_variant 0.11
Rv1258c 1406441 p.Leu300Phe missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417005 p.Phe115Ile missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473843 n.186G>T non_coding_transcript_exon_variant 0.11
inhA 1673844 c.-358G>T upstream_gene_variant 0.11
inhA 1674892 p.Asn231Tyr missense_variant 0.12
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518367 p.Arg85Trp missense_variant 0.11
folC 2746163 p.Arg479Gln missense_variant 0.11
folC 2746990 p.Asp203Glu missense_variant 0.15
ribD 2987091 p.Val85Leu missense_variant 0.13
Rv2752c 3064543 p.Met550Thr missense_variant 0.23
Rv2752c 3064566 c.1626G>T synonymous_variant 0.13
thyX 3067633 p.Ser105Pro missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339504 p.Ile129Met missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640581 c.-954C>T upstream_gene_variant 0.15
fbiA 3641056 p.Trp172Arg missense_variant 0.1
fbiB 3642100 p.Val189Ala missense_variant 0.15
fbiB 3642223 p.Arg230Gln missense_variant 0.12
rpoA 3877891 c.615_616delCG frameshift_variant 0.11
embC 4240813 p.Phe317Leu missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243331 c.99G>T synonymous_variant 0.1
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248191 p.Arg560Cys missense_variant 0.11
embB 4249532 p.Ala1007Thr missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
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