TB-Profiler result

Run: ERR4815985
Summary

Run ID: ERR4815985

Sample name:

Date: 01-04-2023 14:10:47

Number of reads: 3194047

Percentage reads mapped: 95.05

Strain: lineage5.1.2

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
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 1.0
lineage5.1.2 West-Africa 1 AFRI_2;AFRI_3 RD711 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.14 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 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_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
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1407273 p.Asp23Val missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.2
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.16
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.17
rrs 1472135 n.290C>G non_coding_transcript_exon_variant 0.16
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.16
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.16
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.2
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.2
rrs 1472153 n.308G>C non_coding_transcript_exon_variant 0.19
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.3
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.32
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.31
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.3
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.32
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.34
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.3
rrs 1472252 n.407G>C non_coding_transcript_exon_variant 0.24
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.24
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.24
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.26
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.18
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.19
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.21
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.2
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.2
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.2
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.2
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.22
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.22
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.21
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.11
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.15
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.15
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.41
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.42
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.56
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.14
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.52
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.67
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.51
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.51
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.27
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.16
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.2
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.21
rrs 1473008 n.1163C>G non_coding_transcript_exon_variant 0.2
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.24
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.26
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.25
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.28
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.34
rrs 1473070 n.1225G>C non_coding_transcript_exon_variant 0.34
rrs 1473071 n.1226C>A non_coding_transcript_exon_variant 0.36
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.37
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.34
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.17
rrs 1473097 n.1252G>C non_coding_transcript_exon_variant 0.11
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.11
inhA 1673338 c.-864G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 1.0
ndh 2103112 c.-70G>T upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170265 c.347delG frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290062 c.-821G>A upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726261 c.69G>T synonymous_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0
Rv3083 3449644 p.Ala381Thr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3840932 c.489C>T synonymous_variant 1.0
rpoA 3878493 c.15G>A synonymous_variant 1.0
ddn 3986987 c.144G>T synonymous_variant 1.0
ddn 3987180 p.Asp113Asn missense_variant 1.0
clpC1 4040824 c.-120C>T upstream_gene_variant 1.0
embC 4239843 c.-20A>C upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244635 p.Val468Ala missense_variant 1.0
embA 4245147 p.Pro639Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249744 c.3231G>A synonymous_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4326928 c.-621G>A upstream_gene_variant 1.0
ethA 4327103 p.Gly124Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0