TB-Profiler result

Run: ERR2229168
Summary

Run ID: ERR2229168

Sample name:

Date: 31-03-2023 16:46:31

Number of reads: 345462

Percentage reads mapped: 99.35

Strain: lineage4

Drug-resistance: Other

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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
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
gid 4408047 p.Cys52* stop_gained 0.14 streptomycin
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 6486 p.Ala416Asp missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491261 p.Ala160Val missense_variant 0.2
mshA 576060 p.Val238Ala missense_variant 0.36
rpoB 761765 c.1959T>A synonymous_variant 0.5
rpoB 762690 p.Pro962Thr missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.18
mmpL5 777122 c.1359C>T synonymous_variant 0.18
mmpL5 777128 c.1353A>G synonymous_variant 0.18
mmpR5 779009 p.Val7Asp missense_variant 0.18
mmpS5 779572 c.-667G>T upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801278 p.Pro157Gln missense_variant 0.25
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305003 c.2073C>T synonymous_variant 0.22
Rv1258c 1406518 p.Ala275Ser missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472018 n.173G>A non_coding_transcript_exon_variant 0.18
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.13
rrl 1476733 n.3076C>T non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102465 p.Ala193Asp missense_variant 0.4
katG 2155761 p.Asp117Glu missense_variant 0.18
PPE35 2167745 p.Thr956Arg missense_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169192 p.Ala474Val missense_variant 0.33
PPE35 2169269 c.1344A>G synonymous_variant 0.36
PPE35 2169272 c.1341C>G synonymous_variant 0.33
PPE35 2169278 c.1335T>C synonymous_variant 0.42
PPE35 2169281 c.1332T>G synonymous_variant 0.45
PPE35 2169902 c.711G>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.42
PPE35 2170053 p.Thr187Ser missense_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.5
eis 2715286 p.Met16Lys missense_variant 0.25
folC 2746318 c.1281C>A synonymous_variant 0.33
ribD 2987162 c.324C>T synonymous_variant 0.67
thyX 3067880 p.Asp22Glu missense_variant 0.4
fbiD 3338957 c.-161C>A upstream_gene_variant 0.15
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474216 c.210G>A synonymous_variant 0.18
fprA 3474293 p.Arg96Leu missense_variant 0.4
fprA 3474305 p.Val100Glu missense_variant 0.4
clpC1 4039504 p.Asp401Asn missense_variant 0.29
embC 4240038 p.Leu59Ser missense_variant 0.25
embC 4240612 c.750C>A synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244292 c.1060C>T synonymous_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.67
embB 4246555 c.42G>C synonymous_variant 0.75
embB 4246556 p.Ala15Pro missense_variant 0.75
embB 4246563 p.Leu17Trp missense_variant 0.67
embB 4246567 c.54G>T synonymous_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0