TB-Profiler result

Run: SRR11972429
Summary

Run ID: SRR11972429

Sample name:

Date: 03-04-2023 05:41:54

Number of reads: 222930

Percentage reads mapped: 96.33

Strain: lineage2.2

Drug-resistance: RR-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
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
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
gyrB 6636 p.Ser466Phe missense_variant 0.4
gyrA 6922 c.-380G>T upstream_gene_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7513 p.Ala71Asp missense_variant 0.22
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7696 p.Ala132Asp missense_variant 0.17
gyrA 8677 p.Glu459Gly missense_variant 0.22
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 759649 c.-158T>G upstream_gene_variant 0.15
rpoB 759680 c.-127G>T upstream_gene_variant 0.22
rpoB 760378 p.Lys191Met missense_variant 0.18
rpoB 760562 p.Met252Ile missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764819 p.Trp484Gly missense_variant 1.0
rpoC 764968 c.1599T>C synonymous_variant 0.33
rpoC 766931 p.Ala1188Thr missense_variant 0.25
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 781363 c.-197T>G upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.25
fbiC 1303119 c.189G>T synonymous_variant 0.17
Rv1258c 1406473 p.Thr290Ser missense_variant 0.5
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416552 p.Ala266Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471771 n.-75C>A upstream_gene_variant 0.2
rrl 1474396 n.739C>A non_coding_transcript_exon_variant 0.25
rrl 1476027 n.2370G>T non_coding_transcript_exon_variant 0.22
rrl 1476101 n.2444C>A non_coding_transcript_exon_variant 0.4
inhA 1674556 p.Gly119Cys missense_variant 0.33
rpsA 1834177 c.636A>C synonymous_variant 0.88
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154005 p.Glu703* stop_gained 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169386 c.1197_1226delGGGTACCTTCAACACGGGCGGCGCCAACAC disruptive_inframe_deletion 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.67
PPE35 2170053 p.Thr187Ser missense_variant 0.69
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726670 p.Glu160Lys missense_variant 0.25
ribD 2986851 p.Gly5Cys missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612020 p.Gly366Asp missense_variant 0.25
alr 3841244 c.177G>T synonymous_variant 0.25
clpC1 4040496 p.Gly70Val missense_variant 0.15
embC 4241578 c.1716G>T synonymous_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246888 c.375C>T synonymous_variant 0.29
embB 4247533 p.Met340Ile missense_variant 0.2
embB 4247855 p.Gly448Cys missense_variant 0.12
embB 4247934 p.Gly474Asp missense_variant 0.12
embB 4248814 c.2301G>A synonymous_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268021 c.816G>T synonymous_variant 0.67
ethR 4326961 c.-588G>C upstream_gene_variant 0.22
ethR 4326964 c.-585G>A upstream_gene_variant 0.22
ethR 4326970 c.-579G>T upstream_gene_variant 0.22
ethA 4327806 c.-333G>T upstream_gene_variant 0.2
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