TB-Profiler result

Run: SRR21677888
Summary

Run ID: SRR21677888

Sample name:

Date: 04-04-2023 02:49:32

Number of reads: 77306

Percentage reads mapped: 97.26

Strain: lineage4.9;lineage4.1.1

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.93
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.08
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 2153922 c.2189delA frameshift_variant 0.4 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
gyrA 7210 c.-92C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490959 c.177C>A synonymous_variant 0.4
mshA 576389 p.Val348Leu missense_variant 1.0
ccsA 620285 p.Ala132Glu missense_variant 0.67
rpoB 761147 c.1341C>T synonymous_variant 1.0
rpoB 761165 c.1362dupC frameshift_variant 1.0
rpoC 764675 p.Leu436Ile missense_variant 0.67
rpoC 764995 c.1626C>G synonymous_variant 0.5
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777583 p.Tyr300His missense_variant 0.67
mmpL5 777712 p.Gly257Trp missense_variant 1.0
mmpS5 778541 p.Val122Ala missense_variant 0.5
mmpL5 778992 c.-512C>G upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rplC 801200 p.Gly131Val missense_variant 0.67
Rv1258c 1407317 c.24G>A synonymous_variant 0.5
embR 1416250 c.1098C>T synonymous_variant 0.33
embR 1416417 p.Gly311Arg missense_variant 0.22
embR 1417334 p.Ala5Glu missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473912 n.255C>T non_coding_transcript_exon_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102208 p.Gly279Trp missense_variant 0.5
PPE35 2169834 p.Gly260Val missense_variant 0.4
PPE35 2169842 p.Ile257Met missense_variant 0.4
Rv1979c 2223006 c.158delT frameshift_variant 0.29
pncA 2289712 c.-471A>G upstream_gene_variant 0.5
kasA 2518153 p.Ser13Arg missense_variant 0.4
ribD 2987167 p.Gly110Asp missense_variant 0.4
thyX 3067397 p.Ile183Met missense_variant 0.22
thyX 3067530 p.Ala139Val missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087728 c.909C>T synonymous_variant 0.5
fbiD 3339179 p.Ala21Val missense_variant 1.0
fprA 3473822 c.-185C>G upstream_gene_variant 0.29
alr 3841371 p.Gly17Val missense_variant 0.5
panD 4043947 p.Asn112Ser missense_variant 1.0
embC 4241374 c.1513delG frameshift_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244860 p.Gly543Glu missense_variant 1.0
embB 4248630 p.Pro706Gln missense_variant 0.4
ethA 4326124 c.1350T>C synonymous_variant 0.33
ethR 4327027 c.-522C>A upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0