TB-Profiler result

Run: ERR11049468
Summary

Run ID: ERR11049468

Sample name:

Date: 01-04-2023 04:50:08

Number of reads: 4786214

Percentage reads mapped: 99.62

Strain: lineage4.8;lineage4.1.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.65
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.34
lineage4.1.2 Euro-American T;H None 0.63
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.62
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.67
gyrA 9304 p.Gly668Asp missense_variant 0.67
gyrA 9647 c.2346C>G synonymous_variant 0.28
fgd1 491591 p.Lys270Met missense_variant 0.67
mshA 575679 p.Asn111Ser missense_variant 0.6
mshA 576442 p.Cys365Trp missense_variant 0.21
mshA 576456 p.Val370Gly missense_variant 0.22
mshA 576616 c.1269G>C synonymous_variant 0.36
rpoB 760115 c.309C>T synonymous_variant 0.52
rpoC 764367 p.Gly333Ala missense_variant 0.13
rpoC 764537 p.Pro390Ala missense_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 0.69
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.42
fabG1 1673553 p.Asp38Glu missense_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101651 c.1392G>A splice_region_variant&stop_retained_variant 0.3
katG 2154826 p.Pro429Arg missense_variant 0.32
katG 2154828 c.1284G>C synonymous_variant 0.33
PPE35 2168149 p.Pro822Ser missense_variant 0.42
PPE35 2170065 p.Ala183Gly missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.6
kasA 2519071 p.Asp319Glu missense_variant 0.36
ahpC 2726142 c.-51G>A upstream_gene_variant 0.32
pepQ 2860159 p.Ala87Gly missense_variant 0.2
Rv2752c 3064823 p.Val457Leu missense_variant 0.17
Rv2752c 3064875 c.1317C>G synonymous_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 0.67
ald 3086987 p.Gln56His missense_variant 0.23
fbiD 3339734 p.Ala206Gly missense_variant 0.5
fbiD 3339746 p.Ala210Gly missense_variant 0.3
fbiD 3339749 p.Val211Gly missense_variant 0.38
fbiD 3339751 p.Ala212Pro missense_variant 0.19
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.67
fprA 3474119 p.Met38Thr missense_variant 0.32
whiB7 3568428 c.252A>G synonymous_variant 0.43
whiB7 3568431 c.249C>G synonymous_variant 0.22
fbiB 3641031 c.-504C>T upstream_gene_variant 0.32
fbiA 3641477 p.Asp312Gly missense_variant 0.28
rpoA 3878597 c.-90G>C upstream_gene_variant 0.4
rpoA 3878601 c.-94C>G upstream_gene_variant 0.29
rpoA 3878630 c.-123G>C upstream_gene_variant 0.29
rpoA 3878641 c.-134C>G upstream_gene_variant 0.8
embC 4240409 p.Pro183Ala missense_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.64
embB 4246527 p.Ala5Gly missense_variant 0.33
embB 4246529 p.Ser6Arg missense_variant 0.19
embB 4248328 c.1815G>C synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338636 c.-115C>A upstream_gene_variant 0.34