TB-Profiler result

Run: ERR4796584
Summary

Run ID: ERR4796584

Sample name:

Date: 01-04-2023 06:57:12

Number of reads: 2525885

Percentage reads mapped: 93.44

Strain: lineage1.2.2.2

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
lineage1 Indo-Oceanic EAI RD239 0.98
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA RD239 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
gyrB 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7943 p.Glu214Asp missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575629 c.282A>G synonymous_variant 0.12
mshA 575638 c.291T>C synonymous_variant 0.13
mshA 575641 c.294A>G synonymous_variant 0.13
mshA 575674 c.327G>C synonymous_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.36
mshA 576482 p.Val379Leu missense_variant 0.18
rpoC 762989 c.-381G>C upstream_gene_variant 0.15
rpoC 763013 c.-357C>G upstream_gene_variant 0.2
rpoC 763028 c.-342T>C upstream_gene_variant 0.23
rpoC 763031 c.-339T>G upstream_gene_variant 1.0
rpoC 763034 c.-336C>G upstream_gene_variant 0.23
rpoC 763040 c.-330C>G upstream_gene_variant 0.23
rpoC 763070 c.-300T>C upstream_gene_variant 0.25
rpoC 763085 c.-285C>G upstream_gene_variant 0.23
rpoC 763115 c.-255T>C upstream_gene_variant 0.2
rpoC 763136 c.-234C>T upstream_gene_variant 0.18
rpoC 763148 c.-222G>C upstream_gene_variant 0.13
rpoC 763158 c.-212C>T upstream_gene_variant 0.19
rpoC 763166 c.-204A>G upstream_gene_variant 0.17
rpoC 763190 c.-180C>T upstream_gene_variant 0.14
rpoC 763884 p.Ala172Val missense_variant 0.93
rpoC 763886 c.517C>A synonymous_variant 0.92
rpoC 764428 c.1059G>C synonymous_variant 0.12
rpoC 764431 c.1062G>C synonymous_variant 0.12
rpoC 764434 c.1065A>G synonymous_variant 0.13
rpoC 764449 c.1080G>C synonymous_variant 0.14
rpoC 764452 c.1083T>C synonymous_variant 0.14
rpoC 766726 c.3357T>C synonymous_variant 0.15
rpoC 766738 c.3369G>C synonymous_variant 0.16
rpoC 766765 c.3396A>C synonymous_variant 0.15
rpoC 766774 c.3405T>C synonymous_variant 0.14
rpoC 766801 c.3432C>G synonymous_variant 0.13
rpoC 767059 c.3690T>G synonymous_variant 0.12
rpoC 767098 c.3729T>C synonymous_variant 0.12
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 1303884 c.954T>G synonymous_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.15
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.14
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.13
rrl 1473945 n.288T>A non_coding_transcript_exon_variant 0.12
rrl 1473946 n.289A>T non_coding_transcript_exon_variant 0.12
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.12
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.13
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.12
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.14
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.14
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.14
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.12
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.12
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.12
rrl 1476034 n.2377C>A non_coding_transcript_exon_variant 0.12
rpsA 1834633 c.1092A>G synonymous_variant 0.17
rpsA 1834639 c.1098T>C synonymous_variant 0.13
rpsA 1834654 p.Glu371Asp missense_variant 0.13
rpsA 1834684 c.1143C>T synonymous_variant 0.14
rpsA 1834690 c.1149T>C synonymous_variant 0.12
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 2168742 p.Gly624Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4038425 c.2280C>T synonymous_variant 0.97
clpC1 4040517 p.Val63Ala missense_variant 0.92
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.27
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248070 c.1557T>C synonymous_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0