TB-Profiler result

Run: SRR10315661
Summary

Run ID: SRR10315661

Sample name:

Date: 02-04-2023 17:14:37

Number of reads: 5828636

Percentage reads mapped: 97.34

Strain: lineage4.8.1

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
lineage4.8.1 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
rpoB 761139 p.His445Cys missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrl 1476471 n.2814G>T non_coding_transcript_exon_variant 0.12 linezolid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288790 p.Leu151Ser missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
ethA 4326305 p.Ser390Phe missense_variant 1.0 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
mshA 576108 p.Ala254Gly missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474603 n.946C>A non_coding_transcript_exon_variant 0.12
rrl 1474739 n.1082G>T non_coding_transcript_exon_variant 0.13
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.12
rrl 1475454 n.1797G>T non_coding_transcript_exon_variant 0.12
rrl 1475922 n.2265G>T non_coding_transcript_exon_variant 0.14
rrl 1476185 n.2528G>C non_coding_transcript_exon_variant 0.17
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.23
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.27
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.31
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.38
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.28
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.44
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.38
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.38
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.13
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.41
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.41
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.41
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.14
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
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
ribD 2986777 c.-62C>T upstream_gene_variant 1.0
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.37
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
fbiB 3642874 p.Leu447Arg missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0