TB-Profiler result

Run: ERR2513803
Summary

Run ID: ERR2513803

Sample name:

Date: 31-03-2023 19:54:45

Number of reads: 1107361

Percentage reads mapped: 96.36

Strain: lineage3

Drug-resistance: Other

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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
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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 9596 c.2295G>T synonymous_variant 0.97
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
rpoC 763013 c.-357C>G upstream_gene_variant 0.12
rpoC 763025 c.-345C>T upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764181 p.Asp271Gly missense_variant 0.88
rpoC 764188 c.819A>G synonymous_variant 0.12
rpoC 764195 p.Ser276Ile missense_variant 0.13
rpoC 764203 c.834G>C synonymous_variant 0.13
rpoC 764206 c.837T>C synonymous_variant 0.12
rpoC 764215 c.846A>G synonymous_variant 0.12
rpoC 764236 c.867G>A synonymous_variant 0.13
rpoC 765544 c.2175C>G synonymous_variant 0.97
rpoC 766882 c.3513C>T synonymous_variant 0.11
rpoC 766894 c.3525T>C synonymous_variant 0.11
rpoC 766900 c.3531T>C synonymous_variant 0.12
rpoC 766933 c.3564A>G synonymous_variant 0.17
rpoC 766945 c.3576A>G synonymous_variant 0.12
rpoC 766963 c.3594T>C synonymous_variant 0.16
rpoC 766972 c.3603G>C synonymous_variant 0.14
rpoC 766996 c.3627C>T synonymous_variant 0.17
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.17
rpoC 767014 c.3645G>C synonymous_variant 0.17
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.12
rpoC 767059 c.3690T>G synonymous_variant 0.17
rpoC 767062 c.3693C>A synonymous_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
fbiC 1304085 c.1155C>T synonymous_variant 0.15
fbiC 1304091 p.Asp387Glu missense_variant 0.13
fbiC 1304092 p.Met388Leu missense_variant 0.13
fbiC 1304097 c.1167G>C synonymous_variant 0.13
fbiC 1304106 c.1176G>C synonymous_variant 0.13
fbiC 1304127 c.1197A>G synonymous_variant 0.12
fbiC 1304132 p.Ala401Gly missense_variant 0.13
fbiC 1304142 c.1212G>C synonymous_variant 0.14
fbiC 1304161 p.Arg411Ser missense_variant 0.14
fbiC 1304169 c.1239T>C synonymous_variant 0.11
fbiC 1304174 p.Val415Ala missense_variant 0.11
fbiC 1305049 p.Thr707Ser missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.4
rrl 1474702 n.1045G>T non_coding_transcript_exon_variant 0.4
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 2170066 p.Ala183Thr missense_variant 0.18
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
kasA 2518624 c.510C>G synonymous_variant 0.12
kasA 2518639 c.525G>C synonymous_variant 0.12
kasA 2518657 c.543G>C synonymous_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726348 c.156T>C synonymous_variant 0.12
ahpC 2726357 c.165A>G synonymous_variant 0.12
thyX 3067439 c.507A>G synonymous_variant 0.14
thyX 3067445 c.501C>G synonymous_variant 0.14
thyX 3067457 c.489C>G synonymous_variant 0.15
thyX 3067475 c.471A>G synonymous_variant 0.11
thyX 3067490 c.456C>G synonymous_variant 0.13
thyA 3074641 c.-170C>A upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640349 c.-194A>C upstream_gene_variant 1.0
alr 3841069 p.Ile118Phe missense_variant 0.13
rpoA 3878648 c.-141C>A upstream_gene_variant 0.33
embC 4240376 p.Val172Met missense_variant 1.0
embC 4240630 c.768C>A synonymous_variant 0.14
embC 4240632 p.Met257Thr missense_variant 0.14
embC 4240642 c.780G>C synonymous_variant 0.14
embC 4240645 c.783G>C synonymous_variant 0.14
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242511 c.-722G>C upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0