TB-Profiler result

Run: SRR13861242
Summary

Run ID: SRR13861242

Sample name:

Date: 03-04-2023 09:27:00

Number of reads: 553888

Percentage reads mapped: 55.45

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
embB 4247448 p.His312Arg missense_variant 0.15 ethambutol
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 6027 p.His263Arg missense_variant 1.0
gyrA 7835 c.534A>G synonymous_variant 0.13
gyrA 7838 c.537C>G synonymous_variant 0.12
mshA 576327 p.Phe327Tyr missense_variant 1.0
ccsA 620439 c.549T>C synonymous_variant 0.11
ccsA 620445 c.555A>G synonymous_variant 0.11
rpoB 759707 c.-100C>T upstream_gene_variant 1.0
rpoB 760178 c.372G>C synonymous_variant 1.0
rpoB 761222 c.1416G>C synonymous_variant 0.14
rpoB 761249 c.1443A>G synonymous_variant 0.12
rpoB 761255 c.1449T>G synonymous_variant 0.12
rpoB 761261 c.1455G>T synonymous_variant 0.13
rpoB 761327 c.1521A>G synonymous_variant 0.12
rpoB 762284 c.2478G>A synonymous_variant 1.0
rpoC 763594 c.225C>T synonymous_variant 0.12
rpoC 763660 c.291T>G synonymous_variant 0.12
rpoC 763675 c.306C>G synonymous_variant 0.12
rpoC 763696 c.327T>C synonymous_variant 0.12
rpoC 763702 c.333C>G synonymous_variant 0.11
rpoC 763708 c.339G>A synonymous_variant 0.12
rpoC 763709 c.340C>T synonymous_variant 0.12
rpoC 764262 p.Val298Ala missense_variant 0.94
mmpL5 777280 p.Ala401Ser missense_variant 1.0
mmpS5 778853 p.Val18Ala missense_variant 1.0
rplC 800738 c.-71T>C upstream_gene_variant 0.12
rplC 800747 c.-62C>G upstream_gene_variant 0.13
embR 1416662 p.Arg229Pro missense_variant 1.0
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.11
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.12
rrl 1476025 n.2368G>T non_coding_transcript_exon_variant 0.14
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.12
rrl 1476288 n.2631T>C non_coding_transcript_exon_variant 1.0
rpsA 1834297 c.756C>G synonymous_variant 0.13
rpsA 1834303 c.762T>G synonymous_variant 0.13
rpsA 1834306 c.765T>C synonymous_variant 0.12
rpsA 1834348 c.807T>C synonymous_variant 0.12
rpsA 1834366 c.825A>G synonymous_variant 0.12
katG 2155675 p.Arg146Leu missense_variant 1.0
Rv1979c 2222433 c.732A>G synonymous_variant 0.91
thyA 3073989 c.483T>C synonymous_variant 0.13
ald 3086631 c.-189A>G upstream_gene_variant 1.0
fprA 3475014 p.Asp336Glu missense_variant 0.12
fprA 3475015 p.Gln337Lys missense_variant 0.12
fprA 3475019 p.Ser338Thr missense_variant 0.11
fprA 3475022 p.Gly339Ala missense_variant 0.11
fprA 3475036 p.Val344Thr missense_variant 0.11
fprA 3475048 p.Ile348Val missense_variant 0.11
fprA 3475107 c.1101G>C synonymous_variant 0.11
fprA 3475113 c.1107G>C synonymous_variant 0.12
fprA 3475119 c.1113C>T synonymous_variant 0.12
Rv3236c 3612954 c.162delC frameshift_variant 1.0
alr 3840284 p.Trp379* stop_gained 1.0
rpoA 3878217 c.291A>G synonymous_variant 0.11
rpoA 3878220 c.288C>T synonymous_variant 0.11
clpC1 4038923 c.1782A>G synonymous_variant 0.17
clpC1 4038932 c.1773G>C synonymous_variant 0.15
clpC1 4039183 c.1522T>C synonymous_variant 0.12
clpC1 4039517 c.1188C>G synonymous_variant 0.14
clpC1 4039562 c.1143C>G synonymous_variant 0.14
embC 4240042 p.Asn60Lys missense_variant 1.0
embB 4245806 c.-708G>A upstream_gene_variant 0.94
embB 4247075 c.563dupT frameshift_variant 1.0
embB 4247395 c.882C>G synonymous_variant 0.12
embB 4247401 c.888T>C synonymous_variant 0.14
embB 4247437 c.924A>G synonymous_variant 0.15
embB 4247440 c.927C>G synonymous_variant 0.15
embB 4247464 c.951C>G synonymous_variant 0.18
embB 4247839 c.1326G>A synonymous_variant 1.0
embB 4248085 c.1572T>C synonymous_variant 0.13
embB 4248097 c.1584C>G synonymous_variant 0.12
embB 4248133 c.1620C>G synonymous_variant 0.14
embB 4249763 p.Thr1084Pro missense_variant 1.0
ethA 4326860 p.Leu205Pro missense_variant 1.0