TB-Profiler result

Run: SRR16962458
Summary

Run ID: SRR16962458

Sample name:

Date: 03-04-2023 17:48:09

Number of reads: 985092

Percentage reads mapped: 97.9

Strain: lineage4.8

Drug-resistance: Sensitive

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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
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 5472 p.Ala78Val missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.26
mshA 576482 p.Val379Leu missense_variant 0.2
rpoB 762149 c.2343G>T synonymous_variant 0.14
rpoB 762156 p.Val784Ile missense_variant 0.15
rpoB 762173 p.Glu789Asp missense_variant 0.1
rpoB 762176 c.2370T>C synonymous_variant 0.11
rpoB 762177 p.Arg791Cys missense_variant 0.11
rpoB 762181 p.Asp792Ala missense_variant 0.11
rpoB 762185 c.2379G>T synonymous_variant 0.11
rpoB 762197 c.2391C>G synonymous_variant 0.11
rpoB 762200 c.2394C>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460992 c.-53A>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473179 n.1334C>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.11
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.11
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.11
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.14
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.14
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.14
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.11
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.12
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289764 c.-523T>A upstream_gene_variant 0.12
thyX 3067576 p.Asp124Asn missense_variant 0.13
fbiD 3339734 p.Ala206Gly missense_variant 0.57
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568544 p.Cys46Arg missense_variant 0.11
fbiB 3641985 c.453delC frameshift_variant 0.12
alr 3840764 c.657G>C synonymous_variant 1.0
clpC1 4040254 p.Ala151Thr missense_variant 0.11
clpC1 4040282 c.423G>A synonymous_variant 1.0
embC 4241411 p.Ile517Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0