TB-Profiler result

Run: ERR4819993
Summary

Run ID: ERR4819993

Sample name:

Date: 01-04-2023 16:25:19

Number of reads: 236866

Percentage reads mapped: 98.24

Strain:

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
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
gyrB 6853 p.Gln538His missense_variant 0.4 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4408087 c.115delC frameshift_variant 0.67 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
gyrB 5514 p.Gly92Ala missense_variant 0.4
gyrB 6112 p.Met291Ile missense_variant 0.33
gyrB 6124 c.885C>T synonymous_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9383 c.2082T>A synonymous_variant 0.67
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620122 c.236delG frameshift_variant 0.4
ccsA 620241 c.351C>A synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759759 c.-48T>C upstream_gene_variant 0.4
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763667 p.Pro100Ser missense_variant 0.4
rpoC 763942 c.573C>T synonymous_variant 0.5
rpoC 766787 c.3419delA frameshift_variant 0.33
mmpL5 775816 p.Ala889Thr missense_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776199 p.Thr761Ile missense_variant 0.22
mmpL5 778627 c.-147G>A upstream_gene_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303045 c.115C>T synonymous_variant 0.25
Rv1258c 1406242 p.Ala367Thr missense_variant 0.33
Rv1258c 1407284 c.57G>A synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471740 n.-105delT upstream_gene_variant 0.33
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.5
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.33
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.4
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.67
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.67
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.67
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.67
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.67
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.67
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.67
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.67
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.67
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917992 p.Arg18Gln missense_variant 0.5
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155603 p.Asn170Ser missense_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
folC 2747746 c.-148A>C upstream_gene_variant 0.67
ribD 2986865 c.27C>T synonymous_variant 1.0
thyA 3074213 p.Thr87Ala missense_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087511 p.Arg231His missense_variant 0.25
Rv3083 3448890 c.387G>T synonymous_variant 0.5
Rv3083 3449792 p.Ala430Glu missense_variant 0.29
fprA 3473998 c.-9G>A upstream_gene_variant 0.67
fprA 3474597 c.591C>A synonymous_variant 0.4
fprA 3475183 p.Ala393Pro missense_variant 0.2
Rv3236c 3612816 p.Ala101Thr missense_variant 0.29
Rv3236c 3612942 p.Ala59Ser missense_variant 0.33
fbiB 3641658 p.Asp42Asn missense_variant 0.22
fbiB 3642314 c.780C>G synonymous_variant 0.25
alr 3840824 p.Tyr199* stop_gained 0.5
rpoA 3877581 c.927G>A synonymous_variant 0.67
clpC1 4038864 p.Val614Ala missense_variant 1.0
clpC1 4039385 c.1320C>T synonymous_variant 0.25
clpC1 4040517 p.Val63Ala missense_variant 0.4
clpC1 4040742 c.-38C>T upstream_gene_variant 0.2
embC 4239845 c.-18_-17insC upstream_gene_variant 0.25
embC 4239985 c.123T>C synonymous_variant 0.4
embC 4240151 c.291_292delGC frameshift_variant 1.0
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 0.86
embC 4241819 p.Ser653Arg missense_variant 0.25
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244568 p.Arg446Gly missense_variant 0.29
embB 4247646 p.Glu378Ala missense_variant 0.75
embB 4248846 p.Gly778Asp missense_variant 0.33
embB 4249418 p.Pro969Ala missense_variant 0.33
ubiA 4269031 p.Gly268Asp missense_variant 0.29
ethA 4326759 p.Arg239Trp missense_variant 0.5
ethA 4327058 p.Gly139Asp missense_variant 0.25
ethR 4327804 p.Ala86Thr missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408174 p.Ala10Val missense_variant 0.89
gid 4408312 c.-110C>T upstream_gene_variant 1.0