TB-Profiler result

Run: ERR4828349
Summary

Run ID: ERR4828349

Sample name:

Date: 01-04-2023 18:49:20

Number of reads: 1395154

Percentage reads mapped: 99.25

Strain: lineage1.1.1.1

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 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.99
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.99
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO 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 6112 p.Met291Ile missense_variant 1.0
gyrB 6140 p.Val301Met missense_variant 0.11
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 8650 p.Arg450His missense_variant 0.13
gyrA 8849 c.1548C>G synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490972 p.Arg64Ser missense_variant 1.0
fgd1 491156 p.Phe125Cys missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575320 c.-28C>G upstream_gene_variant 1.0
rpoB 760725 p.Arg307Cys missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.93
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764507 p.Ala380Thr missense_variant 0.12
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775723 p.Ile920Val missense_variant 0.11
mmpL5 775724 c.2757G>C synonymous_variant 0.11
mmpL5 775937 c.2544G>A synonymous_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776916 p.Met522Lys missense_variant 0.12
mmpL5 777136 p.Met449Leu missense_variant 0.11
mmpL5 777581 p.Tyr300* stop_gained 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781420 c.-140C>T upstream_gene_variant 0.12
rplC 801100 p.Gly98Arg missense_variant 1.0
Rv1258c 1406182 p.Ile387Phe missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
rpsA 1834319 p.Val260Ile missense_variant 1.0
rpsA 1834379 p.Gln280* stop_gained 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102469 p.Leu192Met missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155445 p.Val223Met missense_variant 0.12
katG 2156389 c.-278G>C upstream_gene_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.1
PPE35 2167878 p.Ser912Asn missense_variant 0.12
PPE35 2167918 c.2694T>C synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169605 c.1008T>C synonymous_variant 0.2
PPE35 2170086 p.Ala176Gly missense_variant 0.11
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518071 c.-44G>A upstream_gene_variant 0.12
kasA 2518123 c.9G>A synonymous_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714140 p.Thr398Asn missense_variant 1.0
eis 2714914 p.Leu140Pro missense_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2860144 p.Val92Gly missense_variant 0.2
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065143 p.Gly350Glu missense_variant 1.0
thyX 3068133 c.-188G>A upstream_gene_variant 0.14
thyA 3074229 c.243C>T synonymous_variant 0.12
ald 3086780 c.-40T>C upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.17
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448794 c.291G>A synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474054 c.48C>T synonymous_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3640359 c.-184C>T upstream_gene_variant 0.18
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4040027 c.678C>G synonymous_variant 0.1
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 4244096 c.864C>T synonymous_variant 0.96
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326477 c.997C>T synonymous_variant 0.14
whiB6 4338242 p.Gln94Glu 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