TB-Profiler result

Run: SRR7592387
Summary

Run ID: SRR7592387

Sample name:

Date: 04-04-2023 19:51:13

Number of reads: 2356152

Percentage reads mapped: 99.39

Strain: lineage4.8

Drug-resistance: Pre-XDR-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
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
gyrB 6735 p.Asn499Thr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764948 p.Leu527Val missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Met missense_variant 1.0 streptomycin
katG 2155167 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288817 p.Thr142Met missense_variant 1.0 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 5078 c.-162_-161insG upstream_gene_variant 0.41
gyrA 7362 p.Glu21Gln missense_variant 1.0
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 1471939 n.94C>T non_coding_transcript_exon_variant 0.2
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.16
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714217 c.1115dupC frameshift_variant 0.77
eis 2715330 c.3G>A synonymous_variant 0.32
Rv2752c 3064875 c.1317C>G synonymous_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
ald 3087633 c.815_834dupGCGGCTGTTTCGAAGGCTCA frameshift_variant 0.84
fbiD 3339734 p.Ala206Gly missense_variant 0.3
fbiD 3339746 p.Ala210Gly missense_variant 0.24
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474119 p.Met38Thr missense_variant 1.0
fbiA 3641477 p.Asp312Gly missense_variant 1.0
alr 3840489 p.Pro311Arg missense_variant 0.84
rpoA 3878597 c.-90G>C upstream_gene_variant 0.2
rpoA 3878637 c.-130G>C upstream_gene_variant 0.5
rpoA 3878641 c.-134C>G upstream_gene_variant 0.53
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.4
embB 4246584 p.Arg24Pro missense_variant 0.4
ubiA 4269148 p.Val229Ala missense_variant 1.0
ethA 4326533 p.Thr314Ile missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>C upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0