TB-Profiler result

Run: SRR12199439
Summary

Run ID: SRR12199439

Sample name:

Date: 03-04-2023 06:39:41

Number of reads: 464225

Percentage reads mapped: 98.52

Strain: lineage4;lineage1.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 0.06
lineage1 Indo-Oceanic EAI RD239 0.98
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.97
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
ahpC 2726141 c.-52C>T upstream_gene_variant 0.17 isoniazid
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
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620605 c.719delT frameshift_variant 0.17
rpoB 761674 p.Gly623Val missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763083 p.Arg1093Ser missense_variant 0.21
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_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
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461227 c.183G>A synonymous_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
fabG1 1673346 c.-94C>G upstream_gene_variant 0.2
fabG1 1673349 c.-91G>C upstream_gene_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
rpsA 1834319 p.Val260Ile missense_variant 1.0
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 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2167985 p.Met876Ile missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.19
PPE35 2170053 p.Thr187Ser missense_variant 0.19
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
kasA 2519353 p.Phe413Leu missense_variant 0.23
ahpC 2726051 c.-142G>A upstream_gene_variant 0.88
ahpC 2726070 c.-123G>A upstream_gene_variant 0.7
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086750 c.-70A>C upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338920 c.-198G>A upstream_gene_variant 0.88
Rv3083 3448714 p.Asp71His missense_variant 0.8
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 0.9
fbiA 3640366 c.-177G>T upstream_gene_variant 1.0
fbiA 3641206 p.Ala222Thr missense_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239902 p.Leu14Ile missense_variant 0.95
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 0.93
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.43
embB 4246555 c.42G>C synonymous_variant 0.6
embB 4246556 p.Ala15Pro missense_variant 0.6
embB 4246563 p.Leu17Trp missense_variant 0.67
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 4327483 c.-10G>A upstream_gene_variant 1.0
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 0.92