TB-Profiler result

Run: ERR2229574
Summary

Run ID: ERR2229574

Sample name:

Date: 31-03-2023 17:19:48

Number of reads: 1149341

Percentage reads mapped: 99.01

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gyrA 7165 c.-137C>A upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7492 p.Phe64Tyr missense_variant 0.12
fgd1 491026 p.Asn82Asp missense_variant 0.12
rpoB 761290 p.Ser495Leu missense_variant 0.12
rpoC 764056 c.687G>A synonymous_variant 0.13
rpoC 766940 p.Arg1191Ser missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776011 p.Gln824Lys missense_variant 0.12
mmpL5 777149 p.Asn444Lys missense_variant 0.18
mmpL5 777157 c.1324C>A synonymous_variant 0.17
mmpL5 777164 c.1317C>T synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303492 c.562T>C synonymous_variant 0.11
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304484 c.1554C>G synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475450 n.1793C>A non_coding_transcript_exon_variant 0.12
rrl 1476254 n.2597C>A non_coding_transcript_exon_variant 0.12
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.12
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.11
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
fabG1 1673629 p.Asp64His missense_variant 0.11
inhA 1674184 c.-18C>T upstream_gene_variant 0.22
rpsA 1834293 p.Val251Ala missense_variant 0.14
tlyA 1917928 c.-12G>T upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918088 p.Thr50Asn missense_variant 0.12
tlyA 1918203 c.264C>T synonymous_variant 0.2
tlyA 1918293 c.354G>T synonymous_variant 0.17
ndh 2102354 p.Gln230Arg missense_variant 0.2
PPE35 2167865 c.2748G>C synonymous_variant 0.15
PPE35 2167868 c.2745A>C synonymous_variant 0.15
PPE35 2167965 p.Ala883Gly missense_variant 0.2
PPE35 2167967 c.2646A>C synonymous_variant 0.2
PPE35 2168225 c.2388C>A synonymous_variant 0.14
PPE35 2168312 p.Gln767His missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169200 c.1413G>A synonymous_variant 0.22
PPE35 2169902 p.Leu237Phe missense_variant 0.26
PPE35 2169910 p.Asn235Tyr missense_variant 0.24
PPE35 2170048 p.Leu189Val missense_variant 0.43
PPE35 2170053 p.Thr187Ser missense_variant 0.42
PPE35 2170147 p.Ser156Ala missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519116 c.1002C>T synonymous_variant 0.2
eis 2714864 p.Gly157Ser missense_variant 0.18
folC 2746374 p.Pro409Ala missense_variant 0.14
pepQ 2859742 p.Val226Gly missense_variant 0.2
pepQ 2859751 p.Gly223Val missense_variant 0.18
pepQ 2860399 p.Arg7Gln missense_variant 0.12
pepQ 2860616 c.-198G>A upstream_gene_variant 0.17
ribD 2987151 p.His105Asn missense_variant 0.22
Rv2752c 3065155 p.Glu346Gly missense_variant 0.22
Rv2752c 3065242 p.Arg317Gln missense_variant 0.22
thyX 3067594 p.Val118Leu missense_variant 0.15
thyA 3073770 p.Asp234Glu missense_variant 0.14
thyA 3073926 c.546G>A synonymous_variant 0.12
ald 3087485 c.666C>T synonymous_variant 0.12
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fbiA 3641203 p.Gly221Cys missense_variant 0.18
fbiB 3641789 c.255G>T synonymous_variant 0.13
fbiB 3642509 c.977delT frameshift_variant 0.14
alr 3841133 c.288G>A synonymous_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.29
clpC1 4040032 p.Val225Ile missense_variant 0.15
clpC1 4040057 c.648C>T synonymous_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.15
embC 4239957 p.Val32Ala missense_variant 0.11
embA 4242370 c.-863C>T upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246584 p.Arg24Pro missense_variant 0.33
embB 4247034 p.Ser174Asn missense_variant 0.25
aftB 4267976 c.861G>A synonymous_variant 0.14
ubiA 4269990 c.-157G>C upstream_gene_variant 0.14
ethA 4326385 c.1089C>T synonymous_variant 0.13
ethA 4327554 c.-81G>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0