TB-Profiler result

Run: ERR2229709
Summary

Run ID: ERR2229709

Sample name:

Date: 31-03-2023 17:28:00

Number of reads: 506085

Percentage reads mapped: 74.54

Strain: lineage4.8

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
katG 2154441 c.1670delA frameshift_variant 0.13 isoniazid, isoniazid
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 6896 p.Arg553Trp missense_variant 0.29
gyrB 6962 p.Arg575Ser missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
ccsA 620059 p.Asp57Asn missense_variant 0.29
ccsA 620695 p.Phe269Leu missense_variant 0.18
ccsA 620806 p.Asn306Asp missense_variant 0.22
rpoB 760930 p.Val375Ala missense_variant 0.12
rpoB 762739 p.Glu978Ala missense_variant 0.25
rpoC 764756 p.Leu463Ile missense_variant 0.12
rpoC 765231 p.Ala621Val missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776416 p.Phe689Leu missense_variant 0.17
mmpL5 776795 c.1686C>A synonymous_variant 0.33
mmpL5 777637 p.Ile282Val missense_variant 0.12
mmpL5 777647 c.834C>G synonymous_variant 0.12
mmpL5 778068 p.Gly138Asp missense_variant 0.33
mmpL5 778416 p.Pro22Leu missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801320 p.Gly171Asp missense_variant 0.15
fbiC 1303226 p.Arg99Leu missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305441 c.2511C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.25
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
inhA 1674785 p.Arg195Gln missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155138 p.Pro325Gln missense_variant 0.17
katG 2155252 p.Glu287Ala missense_variant 0.29
PPE35 2167739 c.2874C>A synonymous_variant 0.22
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.17
PPE35 2169910 p.Asn235Tyr missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.47
PPE35 2170540 c.73C>T synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519153 p.Ile347Val missense_variant 0.38
folC 2747551 c.48C>T synonymous_variant 0.14
Rv2752c 3065044 p.Phe383Ser missense_variant 0.12
thyA 3074234 p.Trp80Arg missense_variant 0.25
ald 3087546 p.Gly243Cys missense_variant 0.17
fprA 3475223 p.Val406Ala missense_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.19
embC 4240683 p.Asp274Val missense_variant 0.22
embC 4241105 p.Arg415Trp missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243053 p.Thr1064Met missense_variant 0.18
embA 4243435 p.Arg68Leu missense_variant 0.2
embA 4246294 p.Trp1021* stop_gained 0.17
embB 4246544 p.Thr11Pro missense_variant 0.18
embB 4246548 p.Pro12Gln missense_variant 0.53
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4248583 c.2070C>A synonymous_variant 0.13
aftB 4268448 p.Pro130Leu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408088 p.Arg39Cys missense_variant 0.17
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0