TB-Profiler result

Run: ERR2517457

Summary

Run ID: ERR2517457

Sample name:

Date: 31-03-2023 22:12:42

Number of reads: 2496193

Percentage reads mapped: 48.53

Strain: lineage3

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
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9422 c.2121C>T synonymous_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762872 p.Met1022Ile missense_variant 0.1
rpoB 762878 p.Ile1024Met missense_variant 0.1
rpoB 762879 p.Met1025Leu missense_variant 0.11
rpoC 762887 c.-483G>C upstream_gene_variant 0.14
rpoC 762896 c.-474G>C upstream_gene_variant 0.14
rpoC 762917 c.-453C>G upstream_gene_variant 0.16
rpoC 762923 c.-447C>G upstream_gene_variant 0.16
rpoB 762925 p.Thr1040Ile missense_variant 0.15
rpoC 762929 c.-441G>C upstream_gene_variant 0.15
rpoB 762939 p.Met1045Leu missense_variant 0.15
rpoB 762942 p.Ile1046Val missense_variant 0.13
rpoC 762965 c.-405T>C upstream_gene_variant 0.16
rpoC 762980 c.-390T>C upstream_gene_variant 0.14
rpoC 762989 c.-381G>C upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764181 p.Asp271Gly missense_variant 1.0
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.2
rpoC 764410 c.1041G>C synonymous_variant 0.22
rpoC 764428 c.1059G>C synonymous_variant 0.28
rpoC 764434 c.1065A>G synonymous_variant 0.29
rpoC 764435 c.1066A>C synonymous_variant 0.29
rpoC 764446 p.Asp359Glu missense_variant 0.27
rpoC 764450 p.Gly361Arg missense_variant 0.27
rpoC 764458 c.1089G>C synonymous_variant 0.29
rpoC 764461 p.Glu364Asp missense_variant 0.29
rpoC 764468 p.Val367Ile missense_variant 0.3
rpoC 764471 p.Asn368Arg missense_variant 0.3
rpoC 764497 c.1128A>G synonymous_variant 0.25
rpoC 764498 p.Ser377Ala missense_variant 0.23
rpoC 764503 c.1134G>C synonymous_variant 0.23
rpoC 764509 c.1140G>C synonymous_variant 0.23
rpoC 764521 c.1152T>C synonymous_variant 0.11
rpoC 764611 c.1242G>C synonymous_variant 0.19
rpoC 764632 c.1263T>C synonymous_variant 0.23
rpoC 764650 c.1281G>C synonymous_variant 0.24
rpoC 764672 p.Gln435Glu missense_variant 0.25
rpoC 764677 c.1308C>G synonymous_variant 0.24
rpoC 764695 c.1326T>C synonymous_variant 0.24
rpoC 764705 p.Leu446Lys missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.19
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.48
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.57
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.54
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.54
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.54
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.5
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.49
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.5
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.48
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.38
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.13
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.16
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.21
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.21
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.23
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.31
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.31
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.31
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.31
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.29
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.25
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.24
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.23
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.21
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.2
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.11
PPE35 2170053 p.Thr187Ser missense_variant 0.1
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
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 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244454 p.Ala408Ser missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0