TB-Profiler result

Run: SRR6044837
Summary

Run ID: SRR6044837

Sample name:

Date: 04-04-2023 11:48:17

Number of reads: 1959715

Percentage reads mapped: 99.38

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 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288826 p.Val139Ala missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327390 c.83delC frameshift_variant 0.98 ethionamide, 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.97
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764670 p.Pro434Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.98
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
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.33
rrs 1473089 n.1244A>C non_coding_transcript_exon_variant 0.33
rrs 1473091 n.1246G>C non_coding_transcript_exon_variant 0.33
rrs 1473094 n.1249T>A non_coding_transcript_exon_variant 0.33
rrs 1473099 n.1254T>C non_coding_transcript_exon_variant 0.33
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.33
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.33
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.33
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.29
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.25
rrs 1473120 n.1275C>G non_coding_transcript_exon_variant 0.25
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.25
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 0.25
rrs 1473132 n.1287T>C non_coding_transcript_exon_variant 0.25
rrs 1473135 n.1290C>T non_coding_transcript_exon_variant 0.25
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.2
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18
rrl 1473510 n.-148C>A upstream_gene_variant 0.2
rrl 1474130 n.473C>T non_coding_transcript_exon_variant 0.17
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.18
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.15
rrl 1474415 n.758C>T non_coding_transcript_exon_variant 0.22
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.5
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 0.5
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.5
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.6
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 0.5
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 0.43
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.29
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.29
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.33
rrl 1476025 n.2368G>T non_coding_transcript_exon_variant 0.4
rpsA 1834177 c.636A>C synonymous_variant 1.0
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
eis 2714846 p.Val163Ile missense_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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407732 c.471G>A synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0