TB-Profiler result

Run: SRR11972203
Summary

Run ID: SRR11972203

Sample name:

Date: 03-04-2023 05:31:54

Number of reads: 275147

Percentage reads mapped: 99.45

Strain: lineage2.2.1.1

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
gyrA 7582 p.Asp94Gly 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 2289096 p.Asp49Gly missense_variant 0.89 pyrazinamide
embB 4248002 p.Gln497Lys 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
gyrB 7104 p.Trp622* stop_gained 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8298 p.Lys333* stop_gained 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491692 p.Gly304Ser missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575479 c.132G>A synonymous_variant 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761391 p.Glu529Lys missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766480 c.3111C>T synonymous_variant 0.17
rpoC 767196 p.Glu1276Gly missense_variant 0.18
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 777938 c.543T>C synonymous_variant 0.13
mmpL5 778159 p.Phe108Leu missense_variant 0.25
mmpL5 778534 c.-54C>T upstream_gene_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779648 c.-743C>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800641 c.-168T>A upstream_gene_variant 0.18
fbiC 1303625 p.Gly232Val missense_variant 0.29
fbiC 1305206 p.Pro759Leu missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471849 n.4T>C non_coding_transcript_exon_variant 0.17
rrl 1474553 n.896T>C non_coding_transcript_exon_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102144 p.Ala300Val missense_variant 0.12
katG 2154676 p.Ala479Gly missense_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222658 c.507C>T synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518367 p.Arg85Trp missense_variant 0.11
eis 2714846 p.Val163Ile missense_variant 1.0
ahpC 2726225 c.33C>T synonymous_variant 0.14
Rv2752c 3064787 p.Ser469Pro missense_variant 0.22
Rv2752c 3065682 p.Asp170Glu missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449759 p.Thr419Met missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640951 p.Gln137* stop_gained 0.12
fbiB 3641725 p.Pro64His missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244960 c.1728A>G synonymous_variant 0.22
embB 4246823 p.Lys104Glu missense_variant 0.17
embB 4247058 p.Arg182Leu missense_variant 0.25
embB 4248055 c.1542G>A synonymous_variant 0.13
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4249683 p.Trp1057* stop_gained 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269884 c.-51G>A upstream_gene_variant 0.11
ethA 4326406 c.1068C>A synonymous_variant 0.13
whiB6 4338567 c.-46C>A upstream_gene_variant 0.12
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