TB-Profiler result

Run: SRR13837530
Summary

Run ID: SRR13837530

Sample name:

Date: 03-04-2023 09:12:30

Number of reads: 589627

Percentage reads mapped: 95.32

Strain: lineage4.9

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
lineage4.9 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
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 7877 p.His192Gln missense_variant 0.94
mshA 576146 p.Val267Leu missense_variant 1.0
rpoB 759869 c.63C>T synonymous_variant 1.0
rpoC 763402 c.33C>T synonymous_variant 0.11
rpoC 763408 c.39T>C synonymous_variant 0.1
rpoC 763411 c.42T>C synonymous_variant 0.1
rpoC 763414 c.45T>G synonymous_variant 0.1
rpoC 763417 c.48C>G synonymous_variant 0.1
rpoC 763546 c.177A>G synonymous_variant 0.17
rpoC 763570 c.201G>C synonymous_variant 0.15
rpoC 763594 c.225C>T synonymous_variant 0.15
rpoC 763633 c.264T>C synonymous_variant 0.15
rpoC 763657 c.288G>A synonymous_variant 0.12
rpoC 763660 c.291T>G synonymous_variant 0.12
rpoC 763666 c.297G>C synonymous_variant 0.12
rpoC 763669 c.300C>G synonymous_variant 0.12
rpoC 763782 p.Ser138* stop_gained 1.0
rpoC 763945 c.576T>C synonymous_variant 0.15
rpoC 764338 c.969G>A synonymous_variant 0.12
rpoC 764353 c.984G>T synonymous_variant 0.11
rpoC 764568 p.Lys400Thr missense_variant 0.96
rpoC 765379 c.2010G>C synonymous_variant 0.17
rpoC 765382 c.2013G>T synonymous_variant 0.17
rpoC 765383 p.Met672Leu missense_variant 0.17
rpoC 765403 c.2034G>C synonymous_variant 0.14
rpoC 765405 p.Leu679His missense_variant 0.14
rpoC 765409 c.2040T>G synonymous_variant 0.13
rpoC 765421 c.2052C>G synonymous_variant 0.13
rpoC 765449 p.Ala694Ser missense_variant 0.12
rpoC 765454 c.2085C>G synonymous_variant 0.11
rpoC 765907 c.2538G>T synonymous_variant 0.1
rpoC 765910 c.2541G>C synonymous_variant 0.11
rpoC 765967 c.2598C>T synonymous_variant 0.11
rpoC 765973 c.2604C>G synonymous_variant 0.11
rpoC 765979 c.2610C>G synonymous_variant 0.11
rpoC 765982 c.2613C>T synonymous_variant 0.11
rpoC 765994 c.2625A>T synonymous_variant 0.11
rpoC 766003 c.2634G>C synonymous_variant 0.12
rpoC 766009 c.2640G>C synonymous_variant 0.12
rpoC 766012 c.2643C>G synonymous_variant 0.12
rpoC 766931 p.Ala1188Ser missense_variant 0.17
rpoC 766942 c.3573C>T synonymous_variant 0.14
rpoC 766945 c.3576A>C synonymous_variant 0.13
rpoC 767044 c.3675G>C synonymous_variant 0.13
rpoC 767098 c.3729T>C synonymous_variant 0.14
rpoC 767104 c.3735C>G synonymous_variant 0.14
rpoC 767107 c.3738C>T synonymous_variant 0.13
rpoC 767119 c.3750A>G synonymous_variant 0.12
rpoC 767125 c.3756G>C synonymous_variant 0.12
rpoC 767134 c.3765C>T synonymous_variant 0.11
rpoC 767138 c.3769C>T synonymous_variant 0.11
rpoC 767149 c.3780C>T synonymous_variant 0.11
rpoC 767158 c.3789T>C synonymous_variant 0.13
rpoC 767180 p.Ala1271Ser missense_variant 0.12
rpoC 767191 c.3822C>G synonymous_variant 0.12
rpoC 767197 c.3828G>A synonymous_variant 0.12
rpoC 767203 c.3834C>G synonymous_variant 0.12
rpoC 767206 c.3837C>G synonymous_variant 0.12
rpoC 767209 c.3840T>C synonymous_variant 0.12
rpoC 767212 c.3843G>C synonymous_variant 0.12
rpoC 767221 c.3852C>G synonymous_variant 0.12
mmpL5 777073 p.Lys470Glu missense_variant 1.0
mmpL5 777311 c.1170C>T synonymous_variant 1.0
mmpL5 778981 c.-501C>A upstream_gene_variant 1.0
rplC 801436 p.Ser210Arg missense_variant 1.0
fbiC 1303686 c.756C>G synonymous_variant 1.0
rrs 1472605 n.760G>C non_coding_transcript_exon_variant 0.94
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.1
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
inhA 1674376 p.Pro59Ser missense_variant 1.0
rpsA 1833847 c.306C>G synonymous_variant 0.1
tlyA 1917844 c.-96C>A upstream_gene_variant 1.0
tlyA 1918260 p.His107Gln missense_variant 1.0
katG 2154461 p.Ala551Pro missense_variant 1.0
Rv1979c 2222535 c.630C>G synonymous_variant 1.0
kasA 2518608 p.Met165Thr missense_variant 1.0
eis 2714211 c.1122G>A synonymous_variant 1.0
ahpC 2726250 p.Gly20Arg missense_variant 1.0
fprA 3473932 c.-75G>A upstream_gene_variant 1.0
Rv3236c 3612518 p.Tyr200Ser missense_variant 1.0
fbiB 3641684 p.Ser50Arg missense_variant 1.0
rpoA 3877614 c.894G>A synonymous_variant 0.11
rpoA 3877620 c.888G>A synonymous_variant 0.11
rpoA 3877638 c.870T>C synonymous_variant 0.12
rpoA 3877656 c.852T>G synonymous_variant 0.11
rpoA 3877677 c.831G>C synonymous_variant 0.12
rpoA 3877686 c.822A>G synonymous_variant 0.11
rpoA 3877692 c.816G>C synonymous_variant 0.11
clpC1 4039528 c.1177C>A synonymous_variant 0.12
clpC1 4039541 c.1164C>G synonymous_variant 0.12
embC 4240263 p.Val134Ala missense_variant 1.0
embC 4240920 p.Leu353Pro missense_variant 1.0
embC 4241504 p.Val548Met missense_variant 1.0
embB 4248000 p.Asp496Val missense_variant 1.0
aftB 4268715 p.Leu41Pro missense_variant 1.0
ethR 4327704 p.Lys52Asn missense_variant 1.0