TB-Profiler result

Run: ERR4818949
Summary

Run ID: ERR4818949

Sample name:

Date: 01-04-2023 15:50:37

Number of reads: 934270

Percentage reads mapped: 97.66

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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
gyrB 5576 p.Ala113Thr missense_variant 0.12
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 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761930 c.2124G>A synonymous_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765311 p.Ala648Thr missense_variant 0.12
rpoC 767068 c.3699G>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775721 c.2760C>A synonymous_variant 1.0
mmpL5 775741 c.2740C>T synonymous_variant 0.14
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304047 p.Ala373Thr missense_variant 0.12
embR 1416232 p.Cys372Gly missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.4
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.4
rrs 1472123 n.278A>G non_coding_transcript_exon_variant 0.4
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.4
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>G non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 1.0
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.67
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.67
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.5
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.5
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.4
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.4
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.4
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.4
rrs 1473017 n.1172A>G non_coding_transcript_exon_variant 0.75
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.8
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.5
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.38
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.44
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.29
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.29
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.29
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.29
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.33
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.33
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.33
rrs 1473291 n.1446G>A non_coding_transcript_exon_variant 0.29
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.33
rrs 1473316 n.1471C>A non_coding_transcript_exon_variant 0.29
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 0.29
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.29
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.29
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.33
rrl 1475673 n.2020_2021delAA non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101667 p.Ala459Gly missense_variant 0.15
ndh 2102540 p.Ala168Gly missense_variant 0.38
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155504 p.Thr203Asn missense_variant 0.11
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167916 c.2696delT frameshift_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169976 p.Gly213Cys missense_variant 0.12
PPE35 2170362 p.Glu84Gly missense_variant 0.17
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288904 p.Gly113Ala missense_variant 0.1
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726498 p.Asp102Glu missense_variant 0.11
Rv2752c 3065845 p.Cys116Tyr missense_variant 0.12
thyA 3073921 p.Leu184Pro missense_variant 0.11
thyA 3073950 c.522G>T synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449559 p.Met352Ile missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640407 c.-136G>A upstream_gene_variant 0.11
ddn 3986834 c.-10G>T upstream_gene_variant 0.13
clpC1 4039189 p.Arg506Trp missense_variant 0.13
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240373 c.511C>T synonymous_variant 1.0
embC 4241507 p.Ala549Thr missense_variant 0.12
embC 4241562 p.Arg567His missense_variant 0.94
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242153 p.Gly764Asp missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243791 p.Ala187Thr missense_variant 0.15
embA 4244692 p.Tyr487Cys missense_variant 0.14
embA 4246008 p.Arg926Trp missense_variant 0.11
embB 4249235 p.Gly908Arg missense_variant 0.12
aftB 4267740 c.1096delG frameshift_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0