TB-Profiler result

Run: ERR4818962
Summary

Run ID: ERR4818962

Sample name:

Date: 01-04-2023 15:50:54

Number of reads: 243724

Percentage reads mapped: 98.72

Strain: lineage1.1

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 0.96
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 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 5684 c.448delT frameshift_variant 0.14
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 6728 c.-574C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9188 p.Asn629Lys missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.43
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 767141 p.Ile1258Val missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776393 c.2087delT frameshift_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800638 c.-171T>A upstream_gene_variant 0.2
Rv1258c 1406766 p.Gln192Arg missense_variant 0.29
Rv1258c 1407503 c.-164dupT upstream_gene_variant 0.33
embR 1416594 p.Glu252Lys missense_variant 0.18
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461004 c.-41T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471727 n.-119C>T upstream_gene_variant 0.29
rrs 1471750 n.-96A>G upstream_gene_variant 0.29
rrs 1472130 n.285G>T non_coding_transcript_exon_variant 1.0
rpsA 1833619 p.Ile26Met missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101955 p.Gln363Arg missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168133 p.Asp827Gly missense_variant 0.29
PPE35 2168488 p.Ile709Val missense_variant 0.12
Rv1979c 2221979 c.1186T>C synonymous_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222939 p.Gly76Cys missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518151 p.Ser13Arg missense_variant 0.25
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726190 c.-3G>A upstream_gene_variant 0.14
ahpC 2726468 c.276G>A synonymous_variant 1.0
pepQ 2860283 p.Phe46Ile missense_variant 0.22
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065865 p.Leu109Phe missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448582 p.Phe27Leu missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474895 p.Asp297Asn missense_variant 0.5
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568632 c.48G>A synonymous_variant 1.0
whiB7 3568834 c.-155G>T upstream_gene_variant 0.15
fbiA 3640605 c.64delC frameshift_variant 0.15
rpoA 3877695 c.813C>G synonymous_variant 0.14
rpoA 3877704 c.804G>T synonymous_variant 0.18
rpoA 3877728 c.780C>G synonymous_variant 0.17
rpoA 3877731 c.777G>T synonymous_variant 0.17
rpoA 3877734 c.774G>C synonymous_variant 0.17
rpoA 3877737 c.771G>C synonymous_variant 0.17
rpoA 3877743 c.765T>C synonymous_variant 0.18
rpoA 3877749 c.759C>T synonymous_variant 0.2
rpoA 3877758 c.750G>A synonymous_variant 0.2
rpoA 3877764 c.744C>G synonymous_variant 0.25
rpoA 3877776 c.732T>C synonymous_variant 0.2
rpoA 3877782 c.726T>C synonymous_variant 0.25
rpoA 3877785 c.723C>A synonymous_variant 0.25
ddn 3987172 p.Thr110Ile missense_variant 0.33
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246319 c.-195G>A upstream_gene_variant 0.5
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267511 c.1326C>T synonymous_variant 0.22
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327067 p.Leu136Gln missense_variant 0.25
whiB6 4338469 p.Asn18Thr 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 4407789 c.414G>C synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0