TB-Profiler result

Run: ERR4972588
Summary

Run ID: ERR4972588

Sample name:

Date: 01-04-2023 21:48:27

Number of reads: 3069692

Percentage reads mapped: 96.73

Strain: lineage4.3.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 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 761155 p.Ser450Leu missense_variant 0.98 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288930 p.Ser104Arg missense_variant 1.0 pyrazinamide
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490757 c.-26T>A upstream_gene_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.21
mshA 576482 p.Val379Leu missense_variant 0.15
rpoC 764995 c.1626C>G synonymous_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 1472337 n.492C>T non_coding_transcript_exon_variant 0.97
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.1
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.13
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.11
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.11
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.11
rrl 1474450 n.793T>A non_coding_transcript_exon_variant 0.11
rrl 1474454 n.797G>A non_coding_transcript_exon_variant 0.12
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.16
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.13
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.13
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.16
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.15
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.14
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.11
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.11
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.12
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.12
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.12
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.12
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.13
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.13
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.13
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.13
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.13
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.16
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.16
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.15
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.15
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.14
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.11
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.1
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.15
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.16
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.15
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.16
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.15
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.17
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.15
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.15
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.15
rrl 1475963 n.2306G>A non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.1
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.11
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.11
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>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
Rv2752c 3065953 p.Thr80Ile missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841612 c.-193_-192insC upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242402 p.Arg847His missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.44
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0