TB-Profiler result

Run: SRR21677857
Summary

Run ID: SRR21677857

Sample name:

Date: 04-04-2023 02:48:39

Number of reads: 468353

Percentage reads mapped: 99.65

Strain: lineage4.8

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
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
ethA 4327147 p.Trp109* stop_gained 0.17 ethionamide
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 8754 p.Glu485Lys missense_variant 0.13
ccsA 620526 c.636G>T synonymous_variant 0.12
ccsA 620545 p.Leu219Phe missense_variant 0.12
rpoB 759679 c.-128T>C upstream_gene_variant 0.1
rpoB 760881 p.Val359Met missense_variant 0.2
rpoB 762955 p.Pro1050Arg missense_variant 0.12
rpoC 764092 c.723C>T synonymous_variant 0.14
rpoC 764116 c.747C>T synonymous_variant 0.15
rpoC 764375 p.Ala336Thr missense_variant 0.11
rpoC 766343 p.Gly992Ser missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777418 p.Pro355Thr missense_variant 0.14
mmpL5 777868 p.Gln205* stop_gained 0.13
mmpR5 779336 p.Asp116Gly missense_variant 0.11
mmpR5 779360 p.Ala124Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801064 p.Leu86Met missense_variant 0.11
fbiC 1303163 p.Pro78Leu missense_variant 0.14
fbiC 1304674 p.Gly582* stop_gained 0.17
fbiC 1304993 p.Ser688* stop_gained 0.18
Rv1258c 1406818 p.Trp175Arg missense_variant 0.12
atpE 1461168 p.Gln42Lys missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472661 n.816A>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475728 n.2071C>T non_coding_transcript_exon_variant 0.11
fabG1 1673233 c.-207T>G upstream_gene_variant 1.0
fabG1 1673286 c.-154A>G upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102437 c.606G>A synonymous_variant 0.11
katG 2154138 p.Phe658Leu missense_variant 0.15
katG 2154835 p.Tyr426Cys missense_variant 0.1
katG 2156544 c.-433C>G upstream_gene_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.3
PPE35 2170053 p.Thr187Ser missense_variant 0.38
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289765 c.-524T>C upstream_gene_variant 0.13
kasA 2518765 c.651G>A synonymous_variant 0.14
kasA 2519239 c.1125A>C synonymous_variant 0.17
eis 2715432 c.-100C>T upstream_gene_variant 0.11
eis 2715436 c.-104G>A upstream_gene_variant 0.11
eis 2715440 c.-108A>C upstream_gene_variant 0.11
eis 2715445 c.-113C>T upstream_gene_variant 0.11
eis 2715447 c.-115T>A upstream_gene_variant 0.11
eis 2715450 c.-118T>C upstream_gene_variant 0.11
eis 2715451 c.-119C>A upstream_gene_variant 0.11
eis 2715454 c.-122T>G upstream_gene_variant 0.11
eis 2715455 c.-123G>A upstream_gene_variant 0.11
eis 2715458 c.-126T>A upstream_gene_variant 0.1
eis 2715460 c.-128A>G upstream_gene_variant 0.1
folC 2747358 c.239_240delGC frameshift_variant 0.15
folC 2747469 p.Asp44Asn missense_variant 0.14
pepQ 2860226 p.Ala65Ser missense_variant 0.13
ribD 2987154 c.316C>A synonymous_variant 0.13
thyX 3067302 p.Cys215Phe missense_variant 0.12
thyX 3067612 p.Lys112Glu missense_variant 0.11
thyX 3067919 c.27G>T synonymous_variant 0.12
thyA 3074538 c.-67T>C upstream_gene_variant 0.12
ald 3087355 p.Ala179Asp missense_variant 0.12
fprA 3474122 p.Leu39Pro missense_variant 0.29
whiB7 3568862 c.-183C>G upstream_gene_variant 0.11
Rv3236c 3612137 p.Gly327Ala missense_variant 0.18
Rv3236c 3613136 c.-20C>A upstream_gene_variant 0.13
Rv3236c 3613193 c.-77C>A upstream_gene_variant 0.15
fbiB 3642285 p.Leu251Met missense_variant 0.11
alr 3841350 p.Ala24Asp missense_variant 0.12
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4040166 p.Ala180Val missense_variant 0.14
panD 4044422 c.-141C>T upstream_gene_variant 0.12
embC 4239977 p.Leu39Ile missense_variant 0.11
embC 4240646 p.Phe262Ile missense_variant 0.15
embC 4240939 c.1077C>A synonymous_variant 0.14
embC 4242216 p.Phe785Tyr missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243129 c.-104G>A upstream_gene_variant 0.14
embA 4243358 c.126C>A synonymous_variant 0.12
embA 4244375 c.1143C>A synonymous_variant 0.12
embA 4244450 c.1218C>A synonymous_variant 0.11
embA 4245008 p.Phe592Leu missense_variant 0.18
embB 4248197 c.1684C>A synonymous_variant 0.11
embB 4248625 c.2112A>G synonymous_variant 0.11
embB 4248910 c.2397C>T synonymous_variant 0.11
aftB 4267329 p.Arg503Gln missense_variant 0.11
aftB 4267346 c.1491C>T synonymous_variant 0.12
aftB 4267829 c.1008C>T synonymous_variant 0.25
aftB 4267873 p.Gln322Lys missense_variant 0.33
aftB 4267900 p.Ala313Ser missense_variant 0.29
aftB 4268527 p.Arg104Trp missense_variant 0.2
ethA 4327186 p.Arg96Ser missense_variant 0.12
ethR 4328041 p.Thr165Ala missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0