TB-Profiler result

Run: SRR5550401
Summary

Run ID: SRR5550401

Sample name:

Date: 04-04-2023 10:46:20

Number of reads: 591700

Percentage reads mapped: 99.61

Strain: lineage2.2.1.1

Drug-resistance: MDR-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
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
rpoB 761140 p.His445Arg missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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 5305 c.66G>T synonymous_variant 0.17
gyrB 7188 c.1951delC frameshift_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8183 c.882C>G synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9627 p.Ala776Ser missense_variant 0.13
fgd1 491490 c.708C>T synonymous_variant 0.13
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 760013 c.207C>T synonymous_variant 0.12
rpoB 761783 c.1977C>A synonymous_variant 0.13
rpoB 762319 p.Ser838Tyr missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763801 c.432C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 778202 c.-788G>A upstream_gene_variant 0.2
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304870 p.Leu647Pro missense_variant 0.12
fbiC 1305358 c.2430_2431delGC frameshift_variant 0.17
Rv1258c 1406292 p.Gly350Val missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416881 p.Phe156Ser missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471969 n.124T>A non_coding_transcript_exon_variant 0.15
rrl 1474364 n.707G>T non_coding_transcript_exon_variant 0.33
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
inhA 1674912 c.711G>A synonymous_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834455 p.Val305Ala missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102738 c.304delG frameshift_variant 1.0
ndh 2103126 c.-84A>G upstream_gene_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156078 p.Thr12Ala missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518991 p.Arg293Cys missense_variant 0.14
eis 2714846 p.Val163Ile missense_variant 1.0
ribD 2987020 p.Ala61Gly missense_variant 0.12
Rv2752c 3065013 c.1179G>T synonymous_variant 0.12
thyA 3074343 c.128dupC frameshift_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449744 p.Ala414Val missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640603 p.Gln21* stop_gained 0.13
fbiA 3640793 p.Glu84Gly missense_variant 0.17
fbiB 3642614 p.Tyr360* stop_gained 0.15
rpoA 3877671 c.837C>T synonymous_variant 0.12
rpoA 3877817 p.Gly231Cys missense_variant 0.12
clpC1 4040394 p.Gly104Ala missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245131 c.1899G>A synonymous_variant 1.0
embB 4245665 c.-849C>A upstream_gene_variant 0.18
embB 4246544 p.Thr11Pro missense_variant 0.24
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.23
embB 4246556 p.Ala15Pro missense_variant 0.23
embB 4248068 p.Tyr519His missense_variant 0.1
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4249705 c.3192G>A synonymous_variant 0.5
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4268978 p.Leu286Met missense_variant 0.11
ubiA 4269716 c.106_117delCCGCTGGCCGCG conservative_inframe_deletion 0.14
ethA 4327119 p.His119Asn missense_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
gid 4408320 c.-118G>C upstream_gene_variant 0.1