TB-Profiler result

Run: SRR9940998
Summary

Run ID: SRR9940998

Sample name:

Date: 04-04-2023 23:03:48

Number of reads: 507941

Percentage reads mapped: 99.9

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 7830 p.Gly177Trp missense_variant 0.25
fgd1 491083 c.305delT frameshift_variant 0.18
mshA 575722 c.375G>T synonymous_variant 0.18
mshA 575865 c.520delG frameshift_variant 0.15
ccsA 619831 c.-60T>G upstream_gene_variant 0.15
rpoB 760433 p.Asp209Glu missense_variant 0.11
rpoB 761626 p.Arg607Leu missense_variant 0.13
rpoB 761977 p.Asn724Ile missense_variant 0.11
rpoC 764351 p.Val328Leu missense_variant 0.2
rpoC 766690 c.3321G>T synonymous_variant 0.17
mmpL5 775730 c.2751C>T synonymous_variant 0.15
mmpL5 776552 p.Gln643His missense_variant 0.11
mmpL5 776788 p.Glu565Lys missense_variant 0.15
mmpL5 777095 c.1386T>C synonymous_variant 0.2
mmpR5 779030 p.Pro14Leu missense_variant 0.18
mmpR5 779110 p.Gly41Cys missense_variant 0.15
rplC 801133 p.Gly109Cys missense_variant 0.29
Rv1258c 1407318 p.Pro8Arg missense_variant 0.22
embR 1417245 p.Gln35* stop_gained 0.12
atpE 1461087 p.Leu15Met missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472604 n.759A>G non_coding_transcript_exon_variant 0.18
rrs 1472714 n.873dupC non_coding_transcript_exon_variant 0.15
rrs 1473135 n.1290C>A non_coding_transcript_exon_variant 0.15
rrl 1475284 n.1627C>A non_coding_transcript_exon_variant 0.17
rrl 1475356 n.1699A>G non_coding_transcript_exon_variant 0.15
rrl 1476397 n.2740G>A non_coding_transcript_exon_variant 0.15
fabG1 1673175 c.-265G>T upstream_gene_variant 0.14
fabG1 1673379 c.-61A>T upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.41
fabG1 1673391 c.-49T>A upstream_gene_variant 0.15
rpsA 1834280 p.His247Asn missense_variant 0.15
PPE35 2169581 c.1032C>G synonymous_variant 0.17
PPE35 2169587 c.1026G>A synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.31
PPE35 2170598 c.15G>A synonymous_variant 1.0
pncA 2290061 c.-820C>A upstream_gene_variant 0.33
pncA 2290105 c.-864G>A upstream_gene_variant 0.15
kasA 2518151 p.Ser13Arg missense_variant 0.17
kasA 2518157 p.Val15Leu missense_variant 0.18
ahpC 2726656 p.Gly155Val missense_variant 0.13
folC 2747125 p.Met158Ile missense_variant 0.2
folC 2747332 c.267G>T synonymous_variant 0.17
Rv2752c 3065088 c.1104A>T synonymous_variant 0.14
Rv3083 3449654 p.Leu384Gln missense_variant 0.11
Rv3236c 3613271 c.-155T>A upstream_gene_variant 0.17
fbiA 3641132 p.Thr197Ser missense_variant 0.11
rpoA 3878158 p.Thr117Asn missense_variant 0.12
panD 4043940 c.342G>T synonymous_variant 0.12
panD 4044077 p.Ile69Phe missense_variant 0.14
embC 4243113 p.Gly1084Glu missense_variant 0.12
embA 4243375 p.Gly48Ala missense_variant 0.17
embA 4243556 c.324C>T synonymous_variant 0.13
embA 4244544 p.Ala438Thr missense_variant 0.11
embB 4248029 p.Thr506Ser missense_variant 0.2
ubiA 4269227 c.603_606dupCACC frameshift_variant 0.11
ethA 4326589 p.Leu295Phe missense_variant 0.12
ethA 4327139 p.Ala112Glu missense_variant 0.12
ethA 4328007 c.-534G>T upstream_gene_variant 0.14
whiB6 4338693 c.-172A>G upstream_gene_variant 0.17