TB-Profiler result

Run: SRR1723466
Summary

Run ID: SRR1723466

Sample name:

Date: 12-08-2022 16:53:10

Number of reads: 6513065

Percentage reads mapped: 97.03

Strain: lineage2.2.1

Drug-resistance: HR-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
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
katG 2155216 p.Gly299Ala missense_variant 1.0 isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 0.98 isoniazid
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 7673 c.372G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoB 761441 p.Asp545Glu missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776081 c.2400G>A synonymous_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778787 p.Thr40Met 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
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.13
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.16
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.16
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.18
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.18
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.19
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.25
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.26
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.27
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.27
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.19
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.15
rpsA 1833540 c.-2A>G upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154365 p.Ser583Pro missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156552 c.-441C>T upstream_gene_variant 0.98
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987528 c.690A>G synonymous_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.38
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 3878641 c.-134C>G upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246811 p.Gly100Ser missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326676 p.Ser266Arg missense_variant 1.0
whiB6 4338594 c.-73T>A upstream_gene_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