TB-Profiler result

Run: SRR4035719
Summary

Run ID: SRR4035719

Sample name:

Date: 04-04-2023 07:15:24

Number of reads: 1502262

Percentage reads mapped: 99.5

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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 761244 p.Ile480Val missense_variant 0.12 rifampicin
katG 2155740 c.371delG frameshift_variant 0.12 isoniazid, isoniazid
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 5426 p.Thr63Ala missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7657 p.Pro119Arg missense_variant 0.1
gyrA 7694 c.393A>G synonymous_variant 0.11
gyrA 7947 p.Leu216Val missense_variant 0.1
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 576699 p.Glu451Gly missense_variant 0.11
ccsA 620265 c.375C>G synonymous_variant 0.14
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760939 p.Leu378Pro missense_variant 0.13
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766083 p.Ala905Val missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472968 n.1123C>A non_coding_transcript_exon_variant 0.12
rrs 1473017 n.1172A>T non_coding_transcript_exon_variant 0.12
rrl 1473984 n.327T>A non_coding_transcript_exon_variant 0.15
fabG1 1673968 p.Thr177Ala missense_variant 0.12
rpsA 1834211 p.Ala224Pro missense_variant 0.11
tlyA 1917784 c.-156C>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222710 p.Asn152Ile missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289838 c.-597T>C upstream_gene_variant 0.18
pncA 2289847 c.-606C>A upstream_gene_variant 0.17
pncA 2289856 c.-615G>A upstream_gene_variant 0.17
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519098 c.984C>G synonymous_variant 0.12
kasA 2519116 c.1002C>A synonymous_variant 0.17
ahpC 2726371 p.Val60Glu missense_variant 0.13
folC 2747287 c.312G>A synonymous_variant 0.18
Rv2752c 3064924 p.Ala423Gly missense_variant 0.12
Rv2752c 3065072 p.Gly374Cys missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
clpC1 4040294 p.Gln137His missense_variant 0.1
embC 4239883 c.21A>G synonymous_variant 0.12
embC 4242491 p.Arg877Trp missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245504 p.Phe758Leu missense_variant 0.12
whiB6 4338521 c.1A>G start_lost 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0