TB-Profiler result

Run: SRR13837591
Summary

Run ID: SRR13837591

Sample name:

Date: 03-04-2023 09:13:55

Number of reads: 589260

Percentage reads mapped: 99.27

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 2154798 c.1313_1314insT 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
gyrB 5906 p.Val223Leu missense_variant 1.0
gyrB 6011 p.Val258Met missense_variant 1.0
gyrB 6678 p.Pro480Arg missense_variant 1.0
fgd1 490676 c.-107G>C upstream_gene_variant 1.0
mshA 575649 p.Val101Ala missense_variant 0.1
mshA 575674 c.327G>C synonymous_variant 0.14
mshA 575704 c.357T>G synonymous_variant 0.1
mshA 575705 c.358T>C synonymous_variant 0.1
ccsA 620028 c.138G>C synonymous_variant 1.0
ccsA 620226 c.336G>A synonymous_variant 0.12
ccsA 620245 c.355T>C synonymous_variant 0.11
ccsA 620249 p.Ser120Cys missense_variant 0.12
ccsA 620254 c.364_366delCTCinsTTG synonymous_variant 0.11
ccsA 620265 c.375C>G synonymous_variant 0.11
ccsA 620283 c.393T>C synonymous_variant 0.12
ccsA 620284 p.Ala132Pro missense_variant 0.12
ccsA 620288 p.Arg133Gln missense_variant 0.12
ccsA 620295 c.405G>T synonymous_variant 0.12
ccsA 620298 c.408G>C synonymous_variant 0.12
ccsA 620310 c.420C>T synonymous_variant 0.12
ccsA 620317 p.Val143Leu missense_variant 0.12
ccsA 620340 c.450C>G synonymous_variant 0.14
ccsA 620346 c.456C>G synonymous_variant 0.23
ccsA 620362 p.Ala158Thr missense_variant 0.14
ccsA 620367 c.477T>C synonymous_variant 0.13
ccsA 620373 c.483C>G synonymous_variant 0.13
ccsA 620376 c.486G>C synonymous_variant 0.13
ccsA 620385 c.495G>C synonymous_variant 0.12
ccsA 620388 c.498A>G synonymous_variant 0.12
ccsA 620389 c.499C>T synonymous_variant 0.12
ccsA 620412 c.522T>C synonymous_variant 0.14
ccsA 620415 c.525T>C synonymous_variant 0.14
ccsA 620421 c.531G>C synonymous_variant 0.15
ccsA 620424 c.534G>C synonymous_variant 0.15
ccsA 620433 c.543C>G synonymous_variant 0.14
ccsA 620436 c.546T>A synonymous_variant 0.15
ccsA 620439 c.549T>C synonymous_variant 0.18
ccsA 620445 c.555A>G synonymous_variant 0.17
ccsA 620460 c.570T>G synonymous_variant 0.15
ccsA 620461 p.Val191Ile missense_variant 0.17
ccsA 620481 c.591T>G synonymous_variant 0.13
ccsA 620482 p.Val198Leu missense_variant 0.13
rpoB 759638 c.-169T>A upstream_gene_variant 1.0
rpoB 760454 c.650delG frameshift_variant 1.0
rpoC 765487 p.Met706Ile missense_variant 1.0
rpsL 781409 c.-151T>A upstream_gene_variant 1.0
fbiC 1302873 c.-58A>T upstream_gene_variant 1.0
rrs 1471874 n.29A>C non_coding_transcript_exon_variant 1.0
katG 2154654 p.Ser486Arg missense_variant 1.0
katG 2154882 c.1230G>A synonymous_variant 1.0
katG 2155857 c.255C>A synonymous_variant 1.0
PPE35 2170198 p.Ala139Ser missense_variant 1.0
pncA 2290069 c.-828C>T upstream_gene_variant 1.0
eis 2714922 c.411G>A synonymous_variant 1.0
thyA 3074067 c.405C>G synonymous_variant 1.0
alr 3840223 c.1198A>C synonymous_variant 1.0
alr 3840711 p.Ser237Leu missense_variant 1.0
clpC1 4039648 p.Glu353Gln missense_variant 1.0
embC 4242023 p.Val721Leu missense_variant 1.0
embA 4245071 c.1839G>A synonymous_variant 1.0
ethA 4327364 p.Lys37Arg missense_variant 1.0