TB-Profiler result

Run: SRR13837696
Summary

Run ID: SRR13837696

Sample name:

Date: 03-04-2023 09:16:07

Number of reads: 297264

Percentage reads mapped: 97.13

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
gyrA 7066 c.-236G>C upstream_gene_variant 0.17
gyrA 7075 c.-227T>C upstream_gene_variant 0.18
gyrA 7078 c.-224A>C upstream_gene_variant 0.2
gyrA 7084 c.-218A>G upstream_gene_variant 0.2
gyrA 7090 c.-212C>T upstream_gene_variant 0.2
gyrA 7093 c.-209T>G upstream_gene_variant 0.2
gyrA 7099 c.-203G>A upstream_gene_variant 0.2
fgd1 490676 c.-107G>C upstream_gene_variant 1.0
ccsA 620028 c.138G>C synonymous_variant 1.0
rpoB 759638 c.-169T>A upstream_gene_variant 1.0
rpoB 760454 c.650delG frameshift_variant 1.0
rpoB 762233 c.2427G>C synonymous_variant 0.15
rpoB 762246 c.2440C>T synonymous_variant 0.18
rpoB 762254 c.2448T>G synonymous_variant 0.17
rpoB 762257 c.2451C>G synonymous_variant 0.15
rpoB 762266 c.2460T>C synonymous_variant 0.18
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 0.93
rrl 1476382 n.2725A>T non_coding_transcript_exon_variant 0.33
rpsA 1834123 c.582C>G synonymous_variant 0.15
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
ahpC 2726600 c.408T>C synonymous_variant 0.2
thyA 3073874 p.Ile200Val missense_variant 0.18
thyA 3073917 c.555C>G synonymous_variant 0.17
thyA 3073920 c.552C>G synonymous_variant 0.17
thyA 3073925 c.547T>C synonymous_variant 0.17
thyA 3073929 c.543T>C synonymous_variant 0.13
thyA 3073941 c.531C>T synonymous_variant 0.12
thyA 3073953 c.519T>C synonymous_variant 0.13
thyA 3073956 c.516G>C synonymous_variant 0.13
thyA 3073959 c.513T>C synonymous_variant 0.12
thyA 3073983 c.489C>T synonymous_variant 0.12
thyA 3074004 c.468T>C synonymous_variant 0.12
thyA 3074010 c.462C>G synonymous_variant 0.13
thyA 3074028 c.444G>C synonymous_variant 0.12
thyA 3074031 c.441T>C synonymous_variant 0.12
thyA 3074037 c.435C>G synonymous_variant 0.12
thyA 3074067 c.405C>G synonymous_variant 0.94
fbiB 3641791 p.Leu86Trp missense_variant 0.18
alr 3840223 c.1198A>C synonymous_variant 1.0
alr 3840711 p.Ser237Leu missense_variant 1.0
rpoA 3878022 c.486T>C synonymous_variant 0.18
rpoA 3878028 c.480G>C synonymous_variant 0.18
rpoA 3878031 c.477T>C synonymous_variant 0.17
rpoA 3878040 c.468T>C synonymous_variant 0.18
rpoA 3878043 c.465G>A synonymous_variant 0.18
rpoA 3878055 c.453A>G synonymous_variant 0.2
rpoA 3878058 c.450G>T synonymous_variant 0.2
rpoA 3878061 c.447G>C synonymous_variant 0.2
rpoA 3878067 c.441C>G synonymous_variant 0.18
rpoA 3878070 c.438T>C synonymous_variant 0.18
rpoA 3878076 c.432C>T synonymous_variant 0.2
rpoA 3878082 c.426T>G synonymous_variant 0.18
rpoA 3878094 c.414C>G synonymous_variant 0.18
rpoA 3878103 c.405A>G synonymous_variant 0.17
rpoA 3878106 c.402G>C synonymous_variant 0.15
rpoA 3878118 c.390T>C synonymous_variant 0.17
rpoA 3878130 c.378C>G synonymous_variant 0.2
rpoA 3878141 p.Met123Leu missense_variant 0.15
rpoA 3878143 p.Gly122Asp missense_variant 0.15
clpC1 4038530 c.2175G>A synonymous_variant 0.14
clpC1 4039648 p.Glu353Gln missense_variant 0.9
embC 4241530 c.1668C>G synonymous_variant 0.14
embC 4242023 p.Val721Leu missense_variant 1.0
embA 4245071 c.1839G>A synonymous_variant 1.0
embB 4249444 c.2931T>C synonymous_variant 0.13
embB 4249580 p.Leu1023Met missense_variant 0.16
ethA 4327364 p.Lys37Arg missense_variant 1.0