TB-Profiler result

Run: ERR6397155
Summary

Run ID: ERR6397155

Sample name:

Date: 02-04-2023 02:45:09

Number of reads: 3382411

Percentage reads mapped: 87.44

Strain: lineage3

Drug-resistance: HR-TB

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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
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
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 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.32
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764181 p.Asp271Gly missense_variant 1.0
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 1472151 n.306C>A non_coding_transcript_exon_variant 0.11
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.2
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.18
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.17
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.16
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.16
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.13
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.12
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.11
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.19
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.18
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.2
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.33
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.25
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.25
rrs 1472736 n.891G>A non_coding_transcript_exon_variant 0.95
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.12
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.26
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.28
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.27
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.34
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.36
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.37
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.19
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.13
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.12
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.21
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.21
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.21
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.22
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.21
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.2
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.19
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.18
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.19
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.2
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.18
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.18
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.18
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.13
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.12
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.15
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.25
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.27
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.27
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.35
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.34
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.34
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.28
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.21
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.1
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 2170035 p.Val193Ala missense_variant 0.1
PPE35 2170048 p.Leu189Val missense_variant 0.24
PPE35 2170053 p.Thr187Ser missense_variant 0.23
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 1.0
folC 2746810 p.Phe263Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.19
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.28
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.31
embB 4246567 c.54G>T synonymous_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0