TB-Profiler result

Run: ERR4831956
Summary

Run ID: ERR4831956

Sample name:

Date: 01-04-2023 21:13:52

Number of reads: 945314

Percentage reads mapped: 99.41

Strain: lineage2.1

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
lineage2.1 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 761139 p.His445Asp missense_variant 0.96 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289123 c.118delG frameshift_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.64 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
rpoB 761207 c.1401C>A synonymous_variant 0.15
rpoB 762109 p.Pro768Gln missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777663 p.Ala273Gly missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303868 p.Asp313Gly missense_variant 1.0
fbiC 1304443 p.Ala505Thr missense_variant 1.0
Rv1258c 1407473 c.-133C>A upstream_gene_variant 0.15
embR 1417185 p.Leu55Ile missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473874 n.217G>T non_coding_transcript_exon_variant 0.18
rrl 1474076 n.419C>A non_coding_transcript_exon_variant 0.15
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.15
inhA 1674585 c.384T>G synonymous_variant 1.0
rpsA 1833399 c.-143G>T upstream_gene_variant 0.17
rpsA 1833498 c.-44A>G upstream_gene_variant 0.12
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
katG 2156019 p.Glu31Asp missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222902 p.Arg88Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290237 c.-996G>T upstream_gene_variant 0.17
kasA 2518725 p.Ala204Glu missense_variant 0.13
ahpC 2726338 p.Val49Gly missense_variant 0.18
pepQ 2859887 p.Ala178Ser missense_variant 0.12
Rv2752c 3066118 p.Asn25Ser missense_variant 0.1
thyX 3067283 c.663C>A synonymous_variant 0.15
thyX 3067586 c.360C>A synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612471 p.Glu216* stop_gained 0.14
clpC1 4038693 p.Ser671Tyr missense_variant 0.15
clpC1 4039047 p.Gly553Val missense_variant 0.18
embC 4241549 p.Gly563Arg missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244909 c.1677C>T synonymous_variant 0.12
embB 4246088 c.-426A>G upstream_gene_variant 1.0
embB 4249424 c.2912delT frameshift_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268684 p.Gln51His missense_variant 0.13
ubiA 4269742 p.Leu31Pro missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0