TB-Profiler result

Run: SRR6785547
Summary

Run ID: SRR6785547

Sample name:

Date: 04-04-2023 16:03:06

Number of reads: 1162669

Percentage reads mapped: 99.37

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 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 1.0
rpoB 761152 p.Leu449Gln missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778312 p.Gly57Arg missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304944 c.2014C>T synonymous_variant 0.14
Rv1258c 1407518 c.-178C>G upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475299 n.1642G>A non_coding_transcript_exon_variant 0.2
rrl 1475910 n.2253A>T non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154970 p.Asp381Ala missense_variant 0.12
PPE35 2170308 p.Leu102Ala missense_variant 1.0
PPE35 2170313 c.300G>C synonymous_variant 1.0
PPE35 2170392 p.Gly74Ala missense_variant 0.11
PPE35 2170400 c.213G>C synonymous_variant 0.12
PPE35 2170406 c.207A>G synonymous_variant 0.14
PPE35 2170412 c.201G>C synonymous_variant 0.12
PPE35 2170415 c.198A>G synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519140 c.1026G>C synonymous_variant 0.13
kasA 2519143 c.1029G>C synonymous_variant 0.13
ribD 2986910 c.72C>A synonymous_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612936 p.Gly61Ser missense_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.16
rpoA 3878490 c.18C>G synonymous_variant 0.32
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.38
embB 4246555 c.42G>C synonymous_variant 0.6
embB 4246556 p.Ala15Pro missense_variant 0.6
embB 4247512 c.999T>C synonymous_variant 0.14
embB 4247516 p.Asn335Asp missense_variant 0.12
embB 4249594 c.3081G>A synonymous_variant 1.0
ubiA 4269254 p.Ala194Ser missense_variant 0.17
ethR 4326961 c.-588G>C upstream_gene_variant 0.16
ethR 4326964 c.-585G>A upstream_gene_variant 0.16
ethR 4326970 c.-579G>T upstream_gene_variant 0.17
ethR 4326982 c.-567C>G upstream_gene_variant 0.11
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
PPE35 2167034 c.336_*614del frameshift_variant&stop_lost&splice_region_variant 1.0