TB-Profiler result

Run: SRR10315576
Summary

Run ID: SRR10315576

Sample name:

Date: 02-04-2023 17:10:40

Number of reads: 5739013

Percentage reads mapped: 99.07

Strain: lineage4.8;lineage4.1.1.3

Drug-resistance: MDR-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
lineage4.1 Euro-American T;X;H None 0.23
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.76
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.23
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.25
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.81 streptomycin
rrl 1476471 n.2814G>T non_coding_transcript_exon_variant 0.17 linezolid
katG 2155168 p.Ser315Thr missense_variant 0.77 isoniazid
pncA 2289067 p.Ser59Pro missense_variant 0.81 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.75 ethambutol
ethA 4326166 c.1307delC frameshift_variant 0.79 ethionamide, 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
gyrB 6815 p.Lys526Gln missense_variant 0.78
gyrA 7234 c.-68C>T upstream_gene_variant 0.26
gyrA 7362 p.Glu21Gln missense_variant 0.99
gyrA 7585 p.Ser95Thr missense_variant 0.26
gyrA 9304 p.Gly668Asp missense_variant 0.2
mshA 576108 p.Ala254Gly missense_variant 0.38
mshA 576482 p.Val379Leu missense_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 0.23
rpoC 766488 p.Pro1040Arg missense_variant 0.19
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 1472332 n.487A>T non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476143 n.2486C>A non_coding_transcript_exon_variant 0.2
rrl 1476173 n.2516A>T non_coding_transcript_exon_variant 0.18
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.12
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.12
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.17
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.18
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.17
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.2
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.21
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.21
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.19
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.16
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.18
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.18
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.26
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.21
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154769 p.Asp448Ala missense_variant 0.75
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.25
fbiD 3339734 p.Ala206Gly missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.15
fbiB 3641807 c.273C>G synonymous_variant 0.31
alr 3840764 c.657G>C synonymous_variant 0.79
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.31
embB 4246584 p.Arg24Pro missense_variant 0.14
embB 4249408 c.2895G>A synonymous_variant 0.17
ethR 4327691 p.Asp48Gly missense_variant 0.27
whiB6 4338595 c.-75delG upstream_gene_variant 1.0