TB-Profiler result

Run: SRR4033462
Summary

Run ID: SRR4033462

Sample name:

Date: 04-04-2023 06:06:53

Number of reads: 1331326

Percentage reads mapped: 99.59

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.97
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 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575897 p.Lys184* stop_gained 0.2
mshA 576044 p.Ala233Thr missense_variant 0.13
rpoC 762971 c.-399G>T upstream_gene_variant 0.14
rpoC 763534 c.165T>C synonymous_variant 0.12
rpoC 763571 p.Val68Met missense_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765337 p.Trp656* stop_gained 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776773 p.His570Asn missense_variant 0.14
mmpL5 776785 p.Glu566* stop_gained 0.15
mmpL5 777243 p.Thr413Ser missense_variant 0.12
mmpL5 777341 c.1140C>G synonymous_variant 0.11
mmpL5 777469 p.Pro338Ser missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416281 p.Arg356Pro missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472466 n.621C>T non_coding_transcript_exon_variant 0.13
rrs 1472475 n.630G>A non_coding_transcript_exon_variant 0.12
rrs 1472561 n.716G>T non_coding_transcript_exon_variant 0.25
rrl 1473579 n.-79T>A upstream_gene_variant 0.15
rrl 1473989 n.332C>T non_coding_transcript_exon_variant 0.12
rrl 1473993 n.336G>A non_coding_transcript_exon_variant 0.13
rrl 1474049 n.392G>A non_coding_transcript_exon_variant 0.13
rrl 1474312 n.655G>A non_coding_transcript_exon_variant 0.17
rrl 1474750 n.1093C>A non_coding_transcript_exon_variant 0.15
rrl 1476308 n.2651G>A non_coding_transcript_exon_variant 0.12
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.15
rpsA 1833466 c.-76C>T upstream_gene_variant 0.17
rpsA 1834633 p.Gln364His missense_variant 0.13
rpsA 1834844 p.Phe435Leu missense_variant 0.13
rpsA 1834853 p.Ala438Thr missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154959 p.Arg385Trp missense_variant 0.13
PPE35 2168798 c.1815T>C synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517927 c.-188G>A upstream_gene_variant 0.12
kasA 2517939 c.-176G>A upstream_gene_variant 0.13
kasA 2519210 p.Val366Ile missense_variant 0.12
eis 2715300 c.33C>T synonymous_variant 0.12
eis 2715357 c.-25G>A upstream_gene_variant 0.18
ahpC 2726449 p.Ser86Leu missense_variant 0.12
ahpC 2726471 p.His93Gln missense_variant 0.2
folC 2746245 p.Ala452Thr missense_variant 0.14
folC 2746438 c.1161G>A synonymous_variant 0.15
folC 2747525 p.Ala25Val missense_variant 0.14
ribD 2986959 c.121T>C synonymous_variant 0.11
ribD 2987058 c.220T>C synonymous_variant 0.11
Rv2752c 3066259 c.-68T>G upstream_gene_variant 0.12
thyA 3073806 c.666C>G synonymous_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074125 p.Leu116Pro missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 c.212delA frameshift_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.91
fprA 3475101 c.1099delG frameshift_variant 0.11
alr 3840580 p.Val281Ile missense_variant 0.13
rpoA 3877719 c.773_788delTGCGGTCCTACAACTG frameshift_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 0.9
clpC1 4038857 c.1848C>A synonymous_variant 0.17
embC 4240345 c.483C>T synonymous_variant 0.14
embC 4240911 p.Ala350Val missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243198 c.-35A>T upstream_gene_variant 0.2
embA 4244659 p.Leu476Pro missense_variant 0.11
embA 4245396 p.Asn722Asp missense_variant 0.11
embA 4245570 c.2339delA frameshift_variant 0.25
embB 4247490 p.Pro326Arg missense_variant 0.12
embB 4248656 p.Ala715Pro missense_variant 0.12
embB 4249273 p.Asp920Glu missense_variant 0.1
ethA 4327351 p.Met41Ile missense_variant 0.14
ethR 4328096 p.Leu183Pro missense_variant 0.11
whiB6 4338352 p.Pro57Leu missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0