TB-Profiler result

Run: ERR2229690
Summary

Run ID: ERR2229690

Sample name:

Date: 31-03-2023 17:25:38

Number of reads: 1112923

Percentage reads mapped: 98.58

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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.33 kanamycin, capreomycin, aminoglycosides, amikacin
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 6918 p.His560Leu missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9742 p.Ala814Val missense_variant 0.15
fgd1 491104 p.Gly108Cys missense_variant 0.25
fgd1 491449 p.Asp223Asn missense_variant 0.17
mshA 575324 c.-24C>A upstream_gene_variant 0.12
mshA 576289 c.942G>C synonymous_variant 0.11
rpoB 760869 p.Val355Phe missense_variant 0.12
rpoB 760894 p.Asp363Ala missense_variant 0.11
rpoB 761966 p.Trp720* stop_gained 0.12
rpoB 762096 p.Thr764Pro missense_variant 0.13
rpoB 762271 p.Lys822Arg missense_variant 0.2
rpoB 762588 p.Thr928Ser missense_variant 0.14
rpoB 762657 p.Ala951Thr missense_variant 0.12
rpoC 764612 p.Gln415* stop_gained 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776181 p.Asp767Val missense_variant 0.12
mmpR5 779035 p.Ile16Val missense_variant 0.12
mmpR5 779255 p.Arg89Gln missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303132 p.Ala68Ser missense_variant 0.11
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406924 p.Leu139Phe missense_variant 0.13
embR 1416700 c.648C>T synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472063 n.218C>T non_coding_transcript_exon_variant 0.29
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.22
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.15
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.38
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.44
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.44
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.62
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.44
fabG1 1673486 p.Arg16Leu missense_variant 0.17
fabG1 1674151 p.Pro238Ala missense_variant 0.12
inhA 1674740 p.Gly180Asp missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155191 c.921A>C synonymous_variant 0.11
katG 2155572 c.540G>A synonymous_variant 0.12
PPE35 2167890 p.Gly908Asp missense_variant 0.11
PPE35 2168260 c.2352delT frameshift_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168967 p.Thr549Lys missense_variant 0.11
PPE35 2169714 p.Gly300Val missense_variant 0.25
PPE35 2170048 p.Leu189Val missense_variant 0.61
PPE35 2170053 p.Thr187Ser missense_variant 0.62
PPE35 2170333 p.Val94Met missense_variant 0.13
Rv1979c 2223031 p.Pro45Leu missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715432 c.-100C>T upstream_gene_variant 0.12
eis 2715436 c.-104G>A upstream_gene_variant 0.13
folC 2747325 p.Arg92Cys missense_variant 0.13
folC 2747369 p.Ser77* stop_gained 0.12
ribD 2987034 p.Gly66Cys missense_variant 0.15
ribD 2987473 p.Cys212Phe missense_variant 0.11
ribD 2987480 c.642G>A synonymous_variant 0.12
Rv2752c 3065934 p.His86Gln missense_variant 0.11
Rv2752c 3067094 c.-903C>T upstream_gene_variant 0.11
Rv2752c 3067176 c.-985A>T upstream_gene_variant 0.11
thyX 3067340 c.606G>A synonymous_variant 0.15
ald 3087811 p.Ala331Val missense_variant 0.18
fbiB 3642663 p.Val377Phe missense_variant 0.13
alr 3840688 c.732delC frameshift_variant 0.12
clpC1 4040057 c.648C>T synonymous_variant 0.13
embC 4240218 p.Arg119His missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243662 p.Asp144Tyr missense_variant 0.12
embA 4244775 p.Met515Leu missense_variant 0.12
embA 4245853 p.Ala874Asp missense_variant 0.17
embA 4246086 p.Gln952Lys missense_variant 0.14
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.62
embB 4246555 c.42G>C synonymous_variant 0.7
embB 4246556 p.Ala15Pro missense_variant 0.7
embB 4246563 p.Leu17Trp missense_variant 0.27
embB 4246567 c.54_55insT frameshift_variant 0.18
embB 4246938 p.Ser142Phe missense_variant 0.25
embB 4247028 p.Leu172Arg missense_variant 0.22
embB 4247576 c.1063_1064insA frameshift_variant 0.15
aftB 4268263 p.Ile192Phe missense_variant 0.13
ethR 4327732 p.Tyr62His missense_variant 0.12
whiB6 4338261 c.261G>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0