TB-Profiler result

Run: ERR10796570
Summary

Run ID: ERR10796570

Sample name:

Date: 31-03-2023 11:11:41

Number of reads: 10866613

Percentage reads mapped: 99.99

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 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
katG 2155740 c.371delG frameshift_variant 0.22 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7594 p.Arg98His missense_variant 0.12
gyrA 7984 p.Phe228Ser missense_variant 0.12
mshA 575627 p.Ala94Thr missense_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.32
mshA 576293 p.Ala316Thr missense_variant 0.12
mshA 576549 p.Ala401Val missense_variant 0.25
mshA 576722 p.Val459Leu missense_variant 0.25
ccsA 620643 c.753C>T synonymous_variant 0.12
rpoB 759741 c.-66C>T upstream_gene_variant 0.25
rpoC 764301 p.Gly311Asp missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472439 n.594C>T non_coding_transcript_exon_variant 0.12
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.18
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.18
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.2
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.18
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.25
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.25
rrs 1473208 n.1363G>A non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474773 n.1116C>T non_coding_transcript_exon_variant 0.33
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.36
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.38
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.41
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.11
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.57
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.61
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.52
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.71
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.59
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.67
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.75
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.67
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.48
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518753 p.Met213Ile missense_variant 0.13
kasA 2518984 c.870G>A synonymous_variant 0.11
folC 2746527 c.1071delC frameshift_variant 0.11
fbiD 3338978 c.-140C>T upstream_gene_variant 0.13
fbiD 3339239 p.Ala41Val missense_variant 0.14
fbiD 3339261 c.144C>T synonymous_variant 0.14
fbiA 3640621 p.Gln27Glu missense_variant 0.11
fbiB 3642009 p.Gly159Ser missense_variant 0.2
fbiB 3642110 c.576C>A synonymous_variant 0.2
rpoA 3878661 c.-154T>C upstream_gene_variant 0.15
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4040821 c.-117C>A upstream_gene_variant 0.12
embC 4240644 p.Arg261Gln missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243504 p.Ser91Phe missense_variant 0.22
embA 4244047 p.Ser272Phe missense_variant 0.13
embA 4244853 p.Val541Met missense_variant 0.29
embB 4247942 p.Pro477Ser missense_variant 0.29
embB 4249000 c.2487T>A synonymous_variant 0.12
ethR 4327649 p.Glu34Gly missense_variant 0.11
ethA 4328389 c.-916C>A upstream_gene_variant 0.17
whiB6 4338237 c.285G>A synonymous_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407678 c.525G>A synonymous_variant 0.11
Rv3083 3448498 c.-5_*1408del transcript_ablation 1.0