TB-Profiler result

Run: SRR9940999
Summary

Run ID: SRR9940999

Sample name:

Date: 04-04-2023 23:03:02

Number of reads: 877187

Percentage reads mapped: 99.85

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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
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
mshA 575291 c.-57G>A upstream_gene_variant 0.17
rpoB 760553 c.747C>A synonymous_variant 0.14
mmpS5 778644 p.Trp88Arg missense_variant 0.13
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.13
Rv1258c 1406946 p.Ala132Gly missense_variant 0.13
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471983 n.138C>T non_coding_transcript_exon_variant 0.11
rrl 1474667 n.1010G>A non_coding_transcript_exon_variant 0.11
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.16
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
inhA 1674711 c.510G>A synonymous_variant 0.13
katG 2154063 c.2049C>A synonymous_variant 0.22
PPE35 2167726 p.Val963Met missense_variant 0.13
PPE35 2167934 c.2679G>C synonymous_variant 0.1
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.14
PPE35 2170326 p.Glu96Val missense_variant 0.13
PPE35 2170402 p.Pro71Thr missense_variant 0.12
PPE35 2170598 c.15G>A synonymous_variant 1.0
Rv1979c 2222166 c.999C>T synonymous_variant 0.11
pncA 2289128 c.114G>A synonymous_variant 0.12
pncA 2289263 c.-22C>A upstream_gene_variant 0.14
pncA 2289849 c.-608C>A upstream_gene_variant 0.17
kasA 2518348 c.234A>T synonymous_variant 0.13
eis 2714363 p.Ser324Pro missense_variant 0.1
eis 2714946 c.387C>T synonymous_variant 0.11
eis 2715465 c.-133G>T upstream_gene_variant 0.13
folC 2746523 c.1075delG frameshift_variant 0.17
Rv3083 3448899 c.397delT frameshift_variant 0.11
Rv3083 3449163 c.660G>A synonymous_variant 0.17
fprA 3474343 p.Asn113Asp missense_variant 0.17
alr 3840249 p.Val391Ala missense_variant 0.11
alr 3840338 p.Asp361Glu missense_variant 0.13
clpC1 4039468 p.Arg413Ser missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4246954 c.441C>A synonymous_variant 0.12
embB 4247237 c.724T>C synonymous_variant 0.12
embB 4247533 p.Met340Ile missense_variant 0.15
ethR 4327736 p.Phe63Ser missense_variant 0.1
gid 4408194 c.8delC frameshift_variant 0.11