TB-Profiler result

Run: ERR270671
Summary

Run ID: ERR270671

Sample name:

Date: 31-03-2023 23:08:13

Number of reads: 4560406

Percentage reads mapped: 99.24

Strain: lineage1.1.3.2

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
lineage1 Indo-Oceanic EAI RD239 0.93
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.93
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.92
lineage1.1.3.2 Indo-Oceanic NA RD239 0.91
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
katG 2155168 p.Ser315Thr missense_variant 0.91 isoniazid
ethA 4326419 c.1054delG frameshift_variant 0.94 ethionamide, ethionamide
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 6112 p.Met291Ile missense_variant 0.96
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8188 p.Leu296Pro missense_variant 0.95
gyrA 8452 p.Ala384Val missense_variant 0.9
gyrA 9143 c.1842T>C synonymous_variant 0.93
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619695 c.-196G>A upstream_gene_variant 0.84
rpoB 759746 c.-61C>T upstream_gene_variant 0.18
rpoB 761483 c.1677G>A synonymous_variant 0.89
rpoC 762434 c.-936T>G upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.95
rpoC 763886 c.517C>A synonymous_variant 0.95
rpoC 765171 p.Pro601Leu missense_variant 0.94
rpoC 765230 p.Ala621Thr missense_variant 0.94
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
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417267 c.80dupC frameshift_variant 0.89
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2167983 p.Gly877Asp missense_variant 0.9
Rv1979c 2222308 p.Asp286Gly missense_variant 0.86
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
pncA 2289365 c.-125delC upstream_gene_variant 0.17
kasA 2518132 c.18C>T synonymous_variant 0.91
ahpC 2726051 c.-142G>A upstream_gene_variant 0.93
ahpC 2726105 c.-88G>A upstream_gene_variant 0.15
ahpC 2726515 p.Phe108Ser missense_variant 0.89
ribD 2987307 p.Ala157Pro missense_variant 0.15
Rv2752c 3064632 c.1560C>T synonymous_variant 0.92
thyA 3073806 c.666C>G synonymous_variant 0.29
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 0.95
fprA 3475159 p.Asn385Asp missense_variant 0.94
fbiB 3642173 c.639G>A synonymous_variant 0.9
rpoA 3878687 c.-180A>C upstream_gene_variant 0.92
clpC1 4040517 p.Val63Ala missense_variant 0.95
embC 4240671 p.Thr270Ile missense_variant 0.95
embC 4240807 c.945C>T synonymous_variant 0.93
embC 4241042 p.Asn394Asp missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243701 p.Gly157Cys missense_variant 0.89
embA 4243848 p.Val206Met missense_variant 0.97
embA 4245969 p.Pro913Ser missense_variant 0.93
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248781 c.2268G>A synonymous_variant 0.88
ubiA 4269387 p.Glu149Asp missense_variant 0.9
aftB 4269606 c.-770T>C upstream_gene_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.89
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 0.93
gid 4407792 c.411G>C synonymous_variant 0.91
gid 4407873 c.330G>T synonymous_variant 0.94
gid 4407973 p.Val77Gly missense_variant 0.9