TB-Profiler result

Run: ERR4831840
Summary

Run ID: ERR4831840

Sample name:

Date: 01-04-2023 21:09:19

Number of reads: 1918594

Percentage reads mapped: 98.29

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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
gyrA 7581 p.Asp94Asn missense_variant 0.96 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.97 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 0.97 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
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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.96
rpoC 764923 p.Glu518Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.95
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776510 c.1971C>A synonymous_variant 0.11
mmpL5 776869 c.1612C>A synonymous_variant 0.11
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 1472061 n.216A>T non_coding_transcript_exon_variant 0.29
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.22
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.22
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.22
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.22
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.22
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.2
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.15
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.15
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.22
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.14
rrl 1474613 n.956T>A non_coding_transcript_exon_variant 0.25
rrl 1475031 n.1374G>C non_coding_transcript_exon_variant 0.4
rrl 1475076 n.1419C>A non_coding_transcript_exon_variant 0.22
rrl 1475090 n.1433A>T non_coding_transcript_exon_variant 0.22
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.14
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.15
rrl 1475234 n.1577C>A non_coding_transcript_exon_variant 0.17
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.4
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.29
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.29
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.25
rrl 1475760 n.2105_2106delGC non_coding_transcript_exon_variant 0.29
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.29
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.29
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.25
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.25
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.25
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.14
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.15
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 0.89
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156055 c.57C>A synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289082 p.Pro54Ser missense_variant 0.94
ahpC 2726265 p.Lys25Gln missense_variant 0.23
ahpC 2726338 p.Val49Gly missense_variant 0.23
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
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 4407620 p.Tyr195His missense_variant 0.96
gid 4407927 p.Glu92Asp missense_variant 0.98