TB-Profiler result

Run: ERR270732
Summary

Run ID: ERR270732

Sample name:

Date: 31-03-2023 23:25:31

Number of reads: 1662615

Percentage reads mapped: 99.47

Strain: lineage3.1.2

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.99
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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.97 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 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 576662 p.Ala439Thr missense_variant 0.12
mshA 576673 c.1326G>A synonymous_variant 0.13
ccsA 620065 p.Ala59Thr missense_variant 0.15
ccsA 620086 p.Asp66Asn missense_variant 0.15
rpoB 759746 c.-61C>T upstream_gene_variant 0.98
rpoB 760646 c.840C>T synonymous_variant 0.17
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.95
mmpR5 779215 p.Gln76Glu missense_variant 1.0
mmpL5 779352 c.-872C>T upstream_gene_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303928 p.Ala333Val missense_variant 1.0
Rv1258c 1406897 c.444G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673172 c.-268T>C upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102346 p.Ala233Thr missense_variant 0.16
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726038 c.-155G>A upstream_gene_variant 0.23
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613255 c.-139G>A upstream_gene_variant 1.0
fbiA 3641245 p.Glu235Lys missense_variant 0.13
embC 4240720 p.Phe286Leu missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407980 p.Pro75Ser missense_variant 0.98