TB-Profiler result

Run: ERR4831997
Summary

Run ID: ERR4831997

Sample name:

Date: 01-04-2023 21:15:37

Number of reads: 848161

Percentage reads mapped: 90.39

Strain: lineage2.1

Drug-resistance: MDR-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
lineage2.1 East-Asian (non-Beijing) None None 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 0.94 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289028 p.Cys72Arg missense_variant 1.0 pyrazinamide
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 6016 p.Asp259Glu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.97
gyrA 8168 c.867A>G synonymous_variant 0.13
gyrA 8174 c.873C>G synonymous_variant 0.12
gyrA 8177 c.876A>C synonymous_variant 0.13
gyrA 8186 c.885G>A synonymous_variant 0.13
gyrA 8195 c.894C>A synonymous_variant 0.12
gyrA 8198 c.897T>C synonymous_variant 0.12
gyrA 8207 c.906T>C synonymous_variant 0.12
gyrA 8283 p.Ile328Leu missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761002 p.Thr399Ile missense_variant 0.23
rpoB 761999 c.2193G>C synonymous_variant 0.13
rpoB 762002 c.2196C>G synonymous_variant 0.13
rpoB 762038 c.2232C>T synonymous_variant 0.12
rpoB 762047 c.2241G>A synonymous_variant 0.14
rpoB 762053 c.2247T>C synonymous_variant 0.15
rpoB 762065 c.2259T>C synonymous_variant 0.14
rpoB 762083 c.2277T>C synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.9
rpoC 763594 c.225C>T synonymous_variant 0.15
rpoC 763621 c.252C>G synonymous_variant 0.15
rpoC 763660 c.291T>G synonymous_variant 0.12
rpoC 763666 c.297G>A synonymous_variant 0.12
rpoC 763675 c.306C>G synonymous_variant 0.13
rpoC 763699 c.330G>T synonymous_variant 0.14
rpoC 763702 c.333C>G synonymous_variant 0.14
rpoC 763705 c.336G>C synonymous_variant 0.14
rpoC 763709 c.340C>T synonymous_variant 0.14
rpoC 763714 c.345G>C synonymous_variant 0.14
rpoC 763717 c.348T>C synonymous_variant 0.14
rpoC 763723 c.354G>C synonymous_variant 0.14
rpoC 764819 p.Trp484Gly missense_variant 0.2
rpoC 765121 c.1752G>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778706 p.Val67Gly missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304443 p.Ala505Thr missense_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472743 n.898T>C non_coding_transcript_exon_variant 0.13
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.13
rrl 1474477 n.820C>T non_coding_transcript_exon_variant 0.2
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.25
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.25
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.29
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.33
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 0.29
rrl 1475359 n.1702G>T non_coding_transcript_exon_variant 0.25
rrl 1475427 n.1770C>T non_coding_transcript_exon_variant 0.18
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.15
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.15
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.15
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
PPE35 2168215 p.Thr800Ala missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860120 p.His100Arg missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878172 c.336G>C synonymous_variant 0.14
rpoA 3878193 c.315T>C synonymous_variant 0.13
rpoA 3878196 p.Glu104Ala missense_variant 0.13
rpoA 3878205 c.303T>C synonymous_variant 0.12
rpoA 3878217 c.291A>G synonymous_variant 0.11
rpoA 3878247 c.261G>C synonymous_variant 0.11
rpoA 3878250 c.258C>G synonymous_variant 0.12
rpoA 3878256 c.252G>C synonymous_variant 0.11
rpoA 3878264 p.Ser82Gly missense_variant 0.12
rpoA 3878271 c.237T>C synonymous_variant 0.12
rpoA 3878283 p.Glu75Asp missense_variant 0.12
rpoA 3878298 c.210A>G synonymous_variant 0.12
rpoA 3878310 c.198G>C synonymous_variant 0.13
rpoA 3878313 c.195G>C synonymous_variant 0.13
rpoA 3878322 c.186A>G synonymous_variant 0.13
clpC1 4039064 c.1641C>T synonymous_variant 0.12
clpC1 4039067 c.1638G>C synonymous_variant 0.12
clpC1 4039079 c.1626C>G synonymous_variant 0.12
clpC1 4040841 c.-138delG upstream_gene_variant 1.0
embC 4240418 p.Gly186Cys missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244126 c.894C>T synonymous_variant 1.0
embB 4246088 c.-426A>G upstream_gene_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