TB-Profiler result

Run: SRR10272576
Summary

Run ID: SRR10272576

Sample name:

Date: 02-04-2023 16:42:50

Number of reads: 1101935

Percentage reads mapped: 90.82

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 0.99
lineage4.4.1.1 Euro-American S;Orphans 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
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 575474 p.Asp43Tyr missense_variant 0.12
rpoC 765341 p.Pro658Thr missense_variant 0.11
rpoC 765654 p.Arg762Leu missense_variant 0.12
rpoC 766891 c.3527delT frameshift_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777136 p.Met449Leu missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473936 n.279A>G non_coding_transcript_exon_variant 0.2
rrl 1474489 n.832T>C non_coding_transcript_exon_variant 0.13
rrl 1474755 n.1098G>T non_coding_transcript_exon_variant 0.15
rrl 1475284 n.1627C>T non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.49
PPE35 2170053 p.Thr187Ser missense_variant 0.49
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289970 c.-730delT upstream_gene_variant 0.18
kasA 2518346 c.232C>A synonymous_variant 0.12
kasA 2518864 c.750G>C synonymous_variant 0.14
pepQ 2859613 p.Glu269Val missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475071 p.Tyr355* stop_gained 0.18
fprA 3475357 c.1351T>C synonymous_variant 0.12
Rv3236c 3612155 p.Arg321Leu missense_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.18
embB 4246548 p.Pro12Gln missense_variant 0.24
embB 4246555 c.42G>C synonymous_variant 0.27
embB 4246556 p.Ala15Pro missense_variant 0.27
embB 4246563 p.Leu17Trp missense_variant 0.11
embB 4249498 c.2985G>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408023 c.180A>G synonymous_variant 0.14