TB-Profiler result

Run: SRR9940986
Summary

Run ID: SRR9940986

Sample name:

Date: 04-04-2023 23:02:32

Number of reads: 1100372

Percentage reads mapped: 99.39

Strain: lineage4.9

Drug-resistance: HR-TB

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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
katG 2154100 p.Ser671* stop_gained 0.13 isoniazid
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
fgd1 491016 c.234C>A synonymous_variant 0.14
fgd1 491574 p.Asp264Glu missense_variant 0.22
mshA 576544 c.1197C>A synonymous_variant 0.2
rpoC 764087 p.Leu240Phe missense_variant 0.17
rpoC 764618 p.Leu417Val missense_variant 0.12
rpoC 765026 p.Ala553Ser missense_variant 0.12
rpsL 781524 c.-36C>A upstream_gene_variant 0.13
fbiC 1303016 p.Val29Gly missense_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474131 n.474C>A non_coding_transcript_exon_variant 0.14
rrl 1474282 n.625G>T non_coding_transcript_exon_variant 0.2
rrl 1474482 n.825G>C non_coding_transcript_exon_variant 0.18
rrl 1475425 n.1768G>T non_coding_transcript_exon_variant 0.13
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.17
fabG1 1673993 p.Tyr185Cys missense_variant 0.18
fabG1 1674076 p.Thr213Pro missense_variant 0.26
ndh 2102634 p.Gly137Ser missense_variant 0.13
ndh 2103040 c.3G>T start_lost 0.14
ndh 2103225 c.-183A>C upstream_gene_variant 0.29
katG 2155067 p.Gly349Cys missense_variant 0.15
PPE35 2168759 c.1854C>G synonymous_variant 0.11
PPE35 2170598 c.15G>A synonymous_variant 1.0
whiB7 3568501 p.Ala60Asp missense_variant 0.11
alr 3840612 p.Gly270Val missense_variant 0.16
rpoA 3878623 c.-116C>A upstream_gene_variant 0.13
embC 4240648 c.786C>T synonymous_variant 0.36
embC 4240849 c.987C>T synonymous_variant 0.13
embB 4245650 c.-864C>A upstream_gene_variant 0.12
embB 4247208 p.Ala232Glu missense_variant 0.13
embB 4248884 p.Asn791Asp missense_variant 0.13
aftB 4268588 c.249G>T synonymous_variant 0.22