TB-Profiler result

Run: SRR13837813
Summary

Run ID: SRR13837813

Sample name:

Date: 03-04-2023 09:19:07

Number of reads: 148156

Percentage reads mapped: 97.82

Strain: lineage4.9

Drug-resistance: Other

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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
rrs 1472122 n.277G>C non_coding_transcript_exon_variant 1.0 streptomycin
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
gyrB 5319 p.Arg27Leu missense_variant 1.0
fgd1 491601 c.819T>C synonymous_variant 0.22
rpoB 760867 p.Gly354Asp missense_variant 0.86
rpoB 762496 c.2691delC frameshift_variant 1.0
rpoC 763067 c.-303C>G upstream_gene_variant 0.25
rpoC 763070 c.-300T>C upstream_gene_variant 0.25
rpoC 763115 c.-255T>C upstream_gene_variant 0.29
rpoC 763136 c.-234C>T upstream_gene_variant 0.25
rpoC 763148 c.-222G>C upstream_gene_variant 0.25
rpoC 763158 c.-212C>T upstream_gene_variant 0.25
rpoC 763166 c.-204A>G upstream_gene_variant 0.25
rpoC 763190 c.-180C>T upstream_gene_variant 0.29
rpoC 764793 p.Met475Arg missense_variant 1.0
rpoC 765850 c.2481G>C synonymous_variant 0.25
rpoC 765937 c.2568T>C synonymous_variant 0.25
rpoC 765947 c.2578T>C synonymous_variant 0.33
rpoC 765967 c.2598C>T synonymous_variant 0.29
rpoC 765982 c.2613C>G synonymous_variant 0.25
rpoC 766563 p.Thr1065Ser missense_variant 0.75
mmpL5 775976 c.2505G>C synonymous_variant 1.0
mmpL5 776814 p.Gln556Arg missense_variant 1.0
mmpL5 778077 p.Thr135Ser missense_variant 0.22
rplC 800623 c.-186A>C upstream_gene_variant 1.0
rplC 800769 c.-40A>T upstream_gene_variant 1.0
fbiC 1302878 c.-53C>G upstream_gene_variant 1.0
fbiC 1303535 p.Ser202Leu missense_variant 1.0
atpE 1461256 p.Met71Arg missense_variant 1.0
rrs 1471836 n.-10A>G upstream_gene_variant 1.0
katG 2156157 c.-46C>A upstream_gene_variant 1.0
PPE35 2167713 p.Val967Ala missense_variant 0.4
PPE35 2168627 p.Ile662Met missense_variant 1.0
pncA 2289242 c.-1T>C upstream_gene_variant 1.0
ribD 2987205 p.Ser123Ala missense_variant 1.0
ribD 2987347 p.Pro170Leu missense_variant 1.0
Rv3083 3448903 p.Asp134His missense_variant 1.0
clpC1 4039663 p.Gly348Ser missense_variant 1.0
embC 4241089 c.1227C>G synonymous_variant 0.18
embC 4241095 c.1233C>T synonymous_variant 0.17
embC 4241107 c.1245G>C synonymous_variant 0.15
embC 4241140 c.1278A>G synonymous_variant 0.17
embC 4241146 c.1284C>G synonymous_variant 0.15
embC 4241256 p.Arg465Thr missense_variant 1.0
embA 4246449 p.Val1073Phe missense_variant 1.0
aftB 4268192 c.645G>C synonymous_variant 1.0