TB-Profiler result

Run: SRR6257105
Summary

Run ID: SRR6257105

Sample name:

Date: 04-04-2023 13:26:24

Number of reads: 949108

Percentage reads mapped: 100.0

Strain: lineage2.2.1

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 0.99
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.92 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288956 p.Lys96Gln missense_variant 1.0 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
folC 2747141 p.Glu153Ala missense_variant 1.0 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.94 ethambutol
ethA 4326669 p.Gln269* stop_gained 1.0 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 8399 c.1098T>C synonymous_variant 0.1
gyrA 8420 c.1119T>C synonymous_variant 0.11
gyrA 8423 c.1122G>C synonymous_variant 0.11
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
mshA 576217 p.Leu290Phe missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762167 c.2361T>C synonymous_variant 0.11
rpoB 762176 c.2370T>C synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 0.93
rpoC 765658 c.2289C>T synonymous_variant 0.1
rpoC 766573 c.3204T>C synonymous_variant 0.11
rpoC 766583 p.Gly1072Ser missense_variant 0.12
rpoC 766591 c.3222A>G synonymous_variant 0.12
rpoC 766594 c.3225G>C synonymous_variant 0.12
rpoC 766597 c.3228C>G synonymous_variant 0.1
rpoC 766607 p.Ile1080Leu missense_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
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781760 c.201T>C synonymous_variant 0.1
rpsL 781793 c.234G>C synonymous_variant 0.11
fbiC 1303016 p.Val29Gly missense_variant 0.32
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407005 c.336G>A synonymous_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.11
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.1
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.11
rrl 1474051 n.394T>C non_coding_transcript_exon_variant 0.14
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.1
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834765 c.1224A>G synonymous_variant 0.1
rpsA 1834786 c.1245A>G synonymous_variant 0.1
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
Rv2752c 3065002 p.His397Arg missense_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878559 c.-53delC upstream_gene_variant 0.67
rpoA 3878578 c.-71C>A upstream_gene_variant 1.0
clpC1 4039364 c.1341C>G synonymous_variant 0.11
embC 4240642 c.780G>C synonymous_variant 0.12
embC 4240645 c.783G>C synonymous_variant 0.11
embC 4240654 c.792C>T synonymous_variant 0.12
embC 4240657 c.795G>C synonymous_variant 0.15
embC 4240671 p.Thr270Ile missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249323 p.Ala937Glu missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_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