TB-Profiler result

Run: SRR6785457
Summary

Run ID: SRR6785457

Sample name:

Date: 04-04-2023 15:57:17

Number of reads: 859936

Percentage reads mapped: 99.56

Strain: lineage4.2.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 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 8286 p.Asn329Tyr missense_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 1.0
fgd1 491352 c.570C>T synonymous_variant 0.5
fgd1 491595 c.813C>T synonymous_variant 0.25
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576531 p.Val395Asp missense_variant 0.2
rpoC 764993 p.Ala542Ser missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776582 p.Gln633His missense_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472084 n.239C>A non_coding_transcript_exon_variant 0.25
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.67
fabG1 1673380 c.-60C>G upstream_gene_variant 0.53
fabG1 1673807 p.Ala123Glu missense_variant 0.25
fabG1 1673927 p.Met163Thr missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170308 p.Leu102Ala missense_variant 1.0
PPE35 2170313 c.300G>C synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518879 c.765A>G synonymous_variant 0.14
pepQ 2859678 c.741A>T synonymous_variant 0.23
ribD 2986910 c.72C>A synonymous_variant 1.0
Rv2752c 3065440 p.Ala251Asp missense_variant 0.22
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840689 c.732C>T synonymous_variant 0.17
clpC1 4039121 c.1584T>G synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4249594 c.3081G>A synonymous_variant 1.0
embB 4249647 p.Arg1045Leu missense_variant 0.17
aftB 4267338 p.Leu500Pro missense_variant 0.17
aftB 4269468 c.-632G>A upstream_gene_variant 0.25
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
PPE35 2167025 c.336_*623del frameshift_variant&stop_lost&splice_region_variant 1.0