TB-Profiler result

Run: SRR13837677
Summary

Run ID: SRR13837677

Sample name:

Date: 03-04-2023 09:15:42

Number of reads: 298658

Percentage reads mapped: 96.57

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 6715 c.-587C>T upstream_gene_variant 1.0
fgd1 490833 c.51G>A synonymous_variant 0.14
fgd1 490842 c.60C>G synonymous_variant 0.13
fgd1 490851 c.69A>C synonymous_variant 0.12
fgd1 490890 c.108C>T synonymous_variant 0.17
fgd1 490902 c.120T>C synonymous_variant 0.15
fgd1 490905 c.123T>C synonymous_variant 0.15
fgd1 490911 c.129T>G synonymous_variant 0.15
fgd1 490917 c.135C>A synonymous_variant 0.15
fgd1 490921 p.Gln47Glu missense_variant 0.15
fgd1 490932 c.150T>C synonymous_variant 0.15
fgd1 490948 p.Ser56Ala missense_variant 0.17
fgd1 491121 c.339A>G synonymous_variant 0.33
fgd1 491137 p.Glu119Gln missense_variant 0.4
fgd1 491144 p.Ala121Glu missense_variant 0.4
fgd1 491166 c.384G>C synonymous_variant 0.5
fgd1 491181 c.399T>C synonymous_variant 0.5
fgd1 491191 p.Gly137Arg missense_variant 0.5
fgd1 491194 c.412_414delCTAinsTTG synonymous_variant 0.5
fgd1 491202 c.420G>C synonymous_variant 0.43
fgd1 491203 p.Gln141Glu missense_variant 0.43
fgd1 491212 p.Ser144Arg missense_variant 0.43
fgd1 491217 c.435T>C synonymous_variant 0.43
fgd1 491232 c.450T>C synonymous_variant 0.38
fgd1 491241 p.Asp153Glu missense_variant 0.5
fgd1 491244 c.462T>C synonymous_variant 0.5
fgd1 491259 c.477T>C synonymous_variant 0.33
fgd1 491286 c.504G>C synonymous_variant 0.33
fgd1 491292 c.510G>C synonymous_variant 0.33
fgd1 491295 c.513C>G synonymous_variant 0.33
fgd1 491296 p.Val172Ile missense_variant 0.33
fgd1 491301 c.519C>T synonymous_variant 0.33
mshA 575693 p.Pro116Ala missense_variant 1.0
rpoB 759863 p.Gln19His missense_variant 1.0
rpoB 760399 p.Val198Ala missense_variant 1.0
rpoB 761249 c.1443A>G synonymous_variant 0.15
rpoB 761255 c.1449T>G synonymous_variant 0.15
rpoB 761999 c.2193G>C synonymous_variant 0.18
rpoB 762008 c.2202C>G synonymous_variant 0.17
rpoB 762014 c.2208C>T synonymous_variant 0.21
rpoB 762017 c.2211A>G synonymous_variant 0.14
rpoB 762027 p.Leu741Phe missense_variant 0.12
rpoB 762035 c.2229G>C synonymous_variant 0.12
rpoB 762053 c.2247T>C synonymous_variant 0.11
rpoB 762062 c.2256T>C synonymous_variant 0.12
rpoB 762065 c.2259T>C synonymous_variant 0.12
rpoB 762083 c.2277T>C synonymous_variant 0.13
rpoB 762086 c.2280G>C synonymous_variant 0.13
rpoB 762101 c.2295C>G synonymous_variant 0.19
rpoB 762114 p.Ile770Val missense_variant 0.19
rpoB 762131 c.2325C>G synonymous_variant 0.2
rpoB 762143 c.2337T>C synonymous_variant 0.2
rpoB 762149 c.2343G>C synonymous_variant 0.17
rpoB 762167 c.2361T>C synonymous_variant 0.17
rpoB 762176 c.2370T>C synonymous_variant 0.17
rpoB 762185 c.2379G>C synonymous_variant 0.18
rpoB 762218 c.2412T>G synonymous_variant 0.13
rpoB 763150 p.Phe1115Tyr missense_variant 1.0
rpoC 764516 p.Asp383Asn missense_variant 1.0
rpoC 764764 c.1395T>C synonymous_variant 0.13
rpoC 766037 p.Asp890Asn missense_variant 0.2
rpoC 766103 p.Arg912Gly missense_variant 1.0
mmpL5 777066 p.Ile472Ser missense_variant 1.0
fbiC 1303584 c.654C>G synonymous_variant 0.17
fbiC 1303590 c.660A>G synonymous_variant 0.17
fbiC 1304559 p.Glu543Asp missense_variant 0.15
fbiC 1304565 c.1635C>G synonymous_variant 0.17
fbiC 1304568 c.1638T>C synonymous_variant 0.17
fbiC 1304574 c.1644C>G synonymous_variant 0.15
fbiC 1304580 c.1650T>C synonymous_variant 0.15
fbiC 1304628 c.1698G>C synonymous_variant 0.14
fbiC 1304634 c.1704C>G synonymous_variant 0.17
fbiC 1304640 c.1710A>C synonymous_variant 0.15
fbiC 1304646 c.1716T>C synonymous_variant 0.15
fbiC 1304658 c.1728C>G synonymous_variant 0.15
fbiC 1304670 c.1740G>T synonymous_variant 0.13
fbiC 1304671 p.Val581Ile missense_variant 0.13
fbiC 1304675 p.Gly582Glu missense_variant 0.12
fbiC 1304691 c.1761G>C synonymous_variant 0.13
fbiC 1304703 c.1773C>G synonymous_variant 0.14
rrl 1474051 n.394T>C non_coding_transcript_exon_variant 0.13
rrl 1474054 n.397T>C non_coding_transcript_exon_variant 0.13
rrl 1474056 n.399T>C non_coding_transcript_exon_variant 0.13
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.12
rrl 1474104 n.447G>A non_coding_transcript_exon_variant 0.12
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.13
rrl 1474112 n.455T>A non_coding_transcript_exon_variant 0.14
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.17
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.17
rpsA 1833554 p.Thr5Ala missense_variant 0.18
rpsA 1833568 c.27G>C synonymous_variant 0.2
rpsA 1833589 c.48A>T synonymous_variant 0.18
rpsA 1833595 c.54T>C synonymous_variant 0.17
rpsA 1833619 c.78A>C synonymous_variant 0.18
rpsA 1833661 c.120A>G synonymous_variant 0.15
rpsA 1833667 c.126C>G synonymous_variant 0.15
rpsA 1834222 c.681T>C synonymous_variant 0.25
rpsA 1834225 c.684C>G synonymous_variant 0.33
rpsA 1834240 c.699T>C synonymous_variant 0.2
rpsA 1834249 c.708T>C synonymous_variant 0.2
rpsA 1834261 c.720A>C synonymous_variant 0.2
rpsA 1834264 c.723G>C synonymous_variant 0.2
rpsA 1834297 c.756C>G synonymous_variant 0.2
rpsA 1834303 c.762T>G synonymous_variant 0.2
rpsA 1834306 c.765T>C synonymous_variant 0.2
ndh 2103185 c.-143A>C upstream_gene_variant 1.0
PPE35 2168894 c.1718dupG frameshift_variant 1.0
PPE35 2170039 p.Ala192Thr missense_variant 1.0
Rv1979c 2221777 p.Ala463Val missense_variant 1.0
kasA 2518793 p.Ser227Thr missense_variant 0.92
ahpC 2726300 c.108C>A synonymous_variant 1.0
folC 2747094 p.Asp169His missense_variant 0.91
Rv2752c 3064936 p.Ser419* stop_gained 1.0
Rv2752c 3065523 c.669C>T synonymous_variant 1.0
Rv2752c 3066039 c.153C>T synonymous_variant 1.0
thyA 3073925 c.547T>C synonymous_variant 0.2
thyA 3073926 c.546G>C synonymous_variant 0.2
thyA 3073929 c.543T>C synonymous_variant 0.2
thyA 3073953 c.519T>C synonymous_variant 0.17
thyA 3073977 c.495A>G synonymous_variant 0.17
thyA 3073989 c.483T>C synonymous_variant 0.18
thyA 3074001 c.471C>G synonymous_variant 0.2
thyA 3074004 c.468T>C synonymous_variant 0.2
thyA 3074010 c.462C>G synonymous_variant 0.2
thyA 3074031 c.441T>C synonymous_variant 0.18
alr 3840469 p.Val318Met missense_variant 0.25
alr 3841286 c.135T>A synonymous_variant 1.0
clpC1 4039368 p.Lys446Thr missense_variant 1.0
embC 4241777 p.Gly639Ser missense_variant 0.92
embB 4248007 c.1494C>G synonymous_variant 0.2
embB 4248011 p.Ser500Ala missense_variant 0.13
embB 4248035 p.Val508Ile missense_variant 0.13
embB 4248041 p.Ala510Thr missense_variant 0.14
embB 4248044 p.Lys511Ala missense_variant 0.14
embB 4248052 c.1539G>A synonymous_variant 0.15
embB 4248055 c.1542G>C synonymous_variant 0.17
embB 4248064 c.1551G>C synonymous_variant 0.14
embB 4248070 c.1557T>C synonymous_variant 0.14
ubiA 4269888 c.-55C>A upstream_gene_variant 1.0