TB-Profiler result

Run: SRR13837600
Summary

Run ID: SRR13837600

Sample name:

Date: 03-04-2023 09:14:20

Number of reads: 2938966

Percentage reads mapped: 95.03

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 2155185 c.926_927insA frameshift_variant 1.0 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
gyrA 8396 p.Tyr365* stop_gained 1.0
fgd1 490821 p.Glu13Asp missense_variant 1.0
mshA 575959 p.Gln204His missense_variant 1.0
rpoC 766364 p.Ala999Ser missense_variant 1.0
mmpL5 775945 p.Val846Leu missense_variant 1.0
mmpL5 778345 p.Leu46Ile missense_variant 1.0
mmpL5 778992 c.-512C>T upstream_gene_variant 1.0
mmpR5 779231 p.Glu81Val missense_variant 1.0
fbiC 1303186 p.Tyr86His missense_variant 1.0
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.15
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.21
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.23
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.24
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.23
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.2
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.15
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.19
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.19
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.19
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.19
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.22
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.19
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.13
fabG1 1673157 c.-283G>C upstream_gene_variant 0.99
ndh 2101749 p.Thr432Ser missense_variant 0.99
katG 2155982 p.Asn44His missense_variant 1.0
PPE35 2168042 c.2571G>C synonymous_variant 1.0
PPE35 2169365 c.1248C>T synonymous_variant 1.0
thyX 3067878 p.Val23Gly missense_variant 1.0
fbiD 3339188 p.Thr24Ser missense_variant 1.0
fprA 3474999 c.993G>T synonymous_variant 1.0
whiB7 3568496 p.Pro62Ser missense_variant 1.0
Rv3236c 3612323 p.Pro265Gln missense_variant 1.0
fbiB 3641121 c.-414C>A upstream_gene_variant 1.0
clpC1 4038346 p.Glu787* stop_gained 1.0
embC 4239894 p.Ala11Gly missense_variant 1.0
ethA 4327073 p.Leu134Pro missense_variant 1.0