TB-Profiler result

Run: SRR4035717
Summary

Run ID: SRR4035717

Sample name:

Date: 04-04-2023 07:15:20

Number of reads: 1455099

Percentage reads mapped: 99.51

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.99
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491456 p.Ile225Thr missense_variant 0.11
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491686 p.Thr302Ala missense_variant 0.11
fgd1 491698 p.Asn306Asp missense_variant 0.12
mshA 576470 p.Gly375Arg missense_variant 0.13
ccsA 619753 c.-138G>A upstream_gene_variant 0.13
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762162 p.Ile786Val missense_variant 0.14
rpoB 763221 p.Ile1139Phe missense_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775684 p.Leu933Ile missense_variant 0.14
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 1471868 n.23T>C non_coding_transcript_exon_variant 0.14
rrs 1472842 n.997G>C non_coding_transcript_exon_variant 0.11
rrl 1473430 n.-228G>T upstream_gene_variant 0.14
rrl 1474050 n.393A>T non_coding_transcript_exon_variant 0.12
rrl 1474068 n.411T>C non_coding_transcript_exon_variant 0.11
rrl 1475183 n.1526A>G non_coding_transcript_exon_variant 0.22
rrl 1475196 n.1539T>C non_coding_transcript_exon_variant 0.18
rrl 1475884 n.2227A>T non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168654 c.1958delA frameshift_variant 0.13
Rv1979c 2221997 p.Pro390Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2746628 p.Asp324Ala missense_variant 0.1
Rv2752c 3064898 p.Val432Leu missense_variant 0.12
Rv2752c 3065586 p.Asp202Glu missense_variant 0.13
Rv2752c 3065616 c.576C>T synonymous_variant 0.14
Rv2752c 3067177 c.-986G>A upstream_gene_variant 0.13
Rv2752c 3067179 c.-988T>C upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339297 c.180T>C synonymous_variant 0.12
fbiD 3339737 p.Thr207Ile missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474145 p.Gly47Arg missense_variant 0.13
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
clpC1 4038423 p.Lys761Met missense_variant 0.14
clpC1 4038909 p.Pro599Leu missense_variant 0.12
clpC1 4040229 p.Gly159Glu missense_variant 0.12
embC 4242608 p.Glu916Gln missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246627 c.114T>C synonymous_variant 0.12
ethA 4326365 p.Lys370Arg missense_variant 0.12
ethA 4326915 p.Ala187Pro missense_variant 0.11
ethA 4327046 p.Tyr143Cys missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407564 c.639A>G synonymous_variant 0.15