TB-Profiler result

Run: SRR6256969
Summary

Run ID: SRR6256969

Sample name:

Date: 04-04-2023 13:21:16

Number of reads: 550547

Percentage reads mapped: 100.0

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 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 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>C upstream_gene_variant 1.0 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
folC 2747471 p.Ile43Thr missense_variant 1.0 para-aminosalicylic_acid
embB 4247429 p.Met306Val 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8956 p.Asp552Gly missense_variant 0.1
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
rpoB 761683 p.Leu626Pro missense_variant 0.12
rpoB 762172 p.Glu789Gly missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
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
fbiC 1303363 p.Phe145Leu missense_variant 0.11
fbiC 1303385 p.Glu152Val missense_variant 0.14
Rv1258c 1406184 p.Pro386Leu missense_variant 0.12
Rv1258c 1406332 p.Gln337* stop_gained 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407458 c.-119delT upstream_gene_variant 0.12
embR 1416870 p.Glu160Lys missense_variant 0.11
embR 1417181 p.Ile56Thr missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473989 n.332C>T non_coding_transcript_exon_variant 0.2
rrl 1475449 n.1792C>T non_coding_transcript_exon_variant 0.11
rpsA 1833965 p.Ile142Val missense_variant 0.17
rpsA 1834157 c.616T>C synonymous_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918406 p.Ser156Leu missense_variant 1.0
ndh 2101764 p.Gly427Arg missense_variant 0.15
katG 2154530 p.Phe528Leu missense_variant 0.11
katG 2154578 p.Gly512Arg missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155214 p.Trp300Arg missense_variant 0.12
PPE35 2167659 p.Thr985Ile missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168290 p.Thr775Ala missense_variant 0.17
PPE35 2169016 p.Thr533Ala missense_variant 1.0
PPE35 2169285 p.Tyr443Cys missense_variant 0.2
PPE35 2169822 p.Ala264Asp missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289130 p.Ala38Pro missense_variant 0.17
eis 2714420 p.Leu305Ile missense_variant 0.1
eis 2714694 c.639A>G synonymous_variant 0.12
eis 2714839 p.Leu165Ser missense_variant 0.12
folC 2746223 p.Asp459Gly missense_variant 0.11
folC 2746747 c.852G>C synonymous_variant 1.0
folC 2747294 p.Gln102Arg missense_variant 0.14
ribD 2986832 c.-6delA upstream_gene_variant 0.11
Rv2752c 3066159 c.32delT frameshift_variant 0.14
thyX 3067936 p.Thr4Ser missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448676 p.Asp58Gly missense_variant 0.1
fprA 3473859 c.-148T>C upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641879 c.345G>T synonymous_variant 0.12
alr 3841174 p.Gly83Arg missense_variant 0.17
embC 4240814 p.Gly318Arg missense_variant 0.1
embC 4242101 p.Lys747Glu missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243121 p.Ser1087Gly missense_variant 0.11
embA 4243230 c.-3C>A upstream_gene_variant 0.1
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243660 p.Ala143Val missense_variant 0.12
embB 4249110 p.Pro866Leu missense_variant 0.11
embB 4249170 p.Asn886Ile missense_variant 0.11
aftB 4267505 c.1332C>T synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326609 p.Trp289Arg missense_variant 0.15
ethA 4327065 p.Cys137Arg missense_variant 1.0
whiB6 4338198 c.323delA frameshift_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