TB-Profiler result

Run: ERR4831987
Summary

Run ID: ERR4831987

Sample name:

Date: 01-04-2023 21:15:14

Number of reads: 836553

Percentage reads mapped: 99.68

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 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
rpoB 761155 p.Ser450Leu missense_variant 0.84 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.89 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.3 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289043 p.Ser67Pro missense_variant 0.6 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.74 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
gyrA 9524 c.2223G>A synonymous_variant 0.89
fgd1 491373 c.591C>A synonymous_variant 0.18
fgd1 491652 c.870C>T synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620754 c.864G>A synonymous_variant 0.12
rpoB 759724 c.-83A>G upstream_gene_variant 0.67
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764918 p.Val517Leu missense_variant 0.7
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777733 p.Leu250Ile missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302804 c.-127G>T upstream_gene_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416744 c.598_603delGAACAC conservative_inframe_deletion 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473717 n.60G>T non_coding_transcript_exon_variant 0.12
rrl 1474515 n.858G>T non_coding_transcript_exon_variant 0.12
rrl 1474888 n.1231C>A non_coding_transcript_exon_variant 0.14
rrl 1474955 n.1298T>A non_coding_transcript_exon_variant 0.2
rrl 1476577 n.2920T>A non_coding_transcript_exon_variant 0.12
fabG1 1673363 c.-77G>T upstream_gene_variant 0.15
inhA 1674662 p.Ala154Glu missense_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834675 c.1134C>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154096 c.2016A>G synonymous_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.31
Rv1979c 2222848 p.Trp106Leu missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289495 c.-254C>G upstream_gene_variant 0.11
kasA 2518407 p.Ala98Asp missense_variant 0.12
kasA 2518689 p.Val192Ala missense_variant 0.1
folC 2746660 c.938delT frameshift_variant 0.29
thyA 3074220 c.252A>G synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087299 p.Met160Ile missense_variant 0.17
ald 3087318 p.Glu167* stop_gained 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611981 p.Ala379Val missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613172 c.-56C>T upstream_gene_variant 0.94
rpoA 3878638 c.-131C>A upstream_gene_variant 0.67
clpC1 4039147 p.Gly520Arg missense_variant 0.13
embC 4241008 c.1146G>T synonymous_variant 0.12
embC 4241050 c.1188T>C synonymous_variant 0.12
embC 4241677 c.1815G>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244859 p.Gly543Trp missense_variant 0.29
embA 4244876 c.1644G>T synonymous_variant 0.4
embA 4244901 p.Ala557Thr missense_variant 0.18
embA 4244942 p.Trp570Cys missense_variant 0.15
embA 4245557 p.Glu775Asp missense_variant 0.15
embB 4247580 p.Ala356Asp missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267699 p.Leu380Met missense_variant 0.18
aftB 4268203 p.Leu212Val missense_variant 0.13
ubiA 4269990 c.-157G>T upstream_gene_variant 0.17
ethA 4326506 p.Thr323Ile missense_variant 0.13
ethA 4326676 p.Ser266Arg missense_variant 0.82
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
gid 4408142 p.Arg21Trp missense_variant 0.16