TB-Profiler result

Run: ERR2229588
Summary

Run ID: ERR2229588

Sample name:

Date: 31-03-2023 17:20:21

Number of reads: 512836

Percentage reads mapped: 98.66

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
gyrB 5446 c.207G>T synonymous_variant 0.14
gyrB 6910 p.Glu557Asp missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8360 c.1059G>A synonymous_variant 0.22
fgd1 491737 c.955C>A synonymous_variant 0.22
mshA 575303 c.-45G>T upstream_gene_variant 0.25
ccsA 620643 c.753C>A synonymous_variant 0.5
rpoB 759985 p.Gly60Ala missense_variant 0.25
rpoB 761302 p.Arg499Pro missense_variant 0.14
rpoB 762385 p.Asn860Ile missense_variant 0.27
rpoB 762954 p.Pro1050Thr missense_variant 0.15
rpoB 763311 p.Glu1169Lys missense_variant 0.18
rpoC 764758 c.1391delA frameshift_variant 0.13
rpoC 765856 c.2487T>C synonymous_variant 0.29
rpoC 766285 c.2916C>T synonymous_variant 0.29
mmpL5 775726 c.2755C>T synonymous_variant 0.5
mmpL5 775727 c.2754C>G synonymous_variant 0.5
mmpL5 775736 c.2745C>G synonymous_variant 0.29
mmpL5 775741 c.2740C>T synonymous_variant 0.29
mmpL5 775742 c.2739C>T synonymous_variant 0.29
mmpL5 775747 p.Met912Leu missense_variant 0.22
mmpL5 776616 p.Pro622Leu missense_variant 0.22
mmpL5 777119 p.His454Gln missense_variant 0.25
mmpL5 777122 c.1359C>T synonymous_variant 0.25
mmpL5 777128 c.1353A>G synonymous_variant 0.25
mmpL5 777157 c.1324C>A synonymous_variant 0.27
mmpL5 777164 c.1317C>T synonymous_variant 0.33
mmpR5 779080 p.Ser31Cys missense_variant 0.18
mmpS5 779656 c.-751G>A upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801449 p.Arg214Gln missense_variant 0.25
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305389 p.Ala820Asp missense_variant 0.29
Rv1258c 1406385 p.Ala319Gly missense_variant 0.22
Rv1258c 1407327 p.Asn5Ile missense_variant 0.14
embR 1416567 p.Asp261Tyr missense_variant 0.17
embR 1416750 p.Glu200Lys missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 0.98
rrl 1474030 n.373G>T non_coding_transcript_exon_variant 0.67
rrl 1475802 n.2145G>A non_coding_transcript_exon_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.44
fabG1 1673924 p.Gly162Asp missense_variant 0.2
rpsA 1834617 p.Ser359Leu missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154329 p.Arg595* stop_gained 0.15
PPE35 2167745 p.Thr956Arg missense_variant 0.3
PPE35 2167997 c.2616G>C synonymous_variant 0.17
PPE35 2168011 p.Ser868Gly missense_variant 0.33
PPE35 2168014 p.Ala867Pro missense_variant 0.33
PPE35 2168015 p.Ile866Val missense_variant 0.33
PPE35 2168024 p.Ala863Pro missense_variant 0.33
PPE35 2168030 c.2583A>G synonymous_variant 0.33
PPE35 2168140 p.Ala825Thr missense_variant 0.29
PPE35 2168143 p.Phe824Leu missense_variant 0.29
PPE35 2168150 c.2463T>C synonymous_variant 0.33
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169611 c.1002C>G synonymous_variant 0.13
PPE35 2169623 c.990T>G synonymous_variant 0.14
PPE35 2169732 p.Asn294Ser missense_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.25
PPE35 2169910 p.Asn235Tyr missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.59
PPE35 2170053 p.Thr187Ser missense_variant 0.59
PPE35 2170392 p.Gly74Ala missense_variant 0.18
PPE35 2170400 c.213G>C synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288716 p.Arg176Cys missense_variant 0.25
pncA 2289290 c.-49C>A upstream_gene_variant 0.17
pncA 2289648 c.-407A>G upstream_gene_variant 0.25
kasA 2518879 c.765A>G synonymous_variant 0.17
kasA 2518882 c.768C>A synonymous_variant 0.17
kasA 2519128 c.1014G>C synonymous_variant 0.33
kasA 2519131 c.1017G>C synonymous_variant 0.33
kasA 2519140 c.1026G>C synonymous_variant 0.4
kasA 2519143 c.1029G>C synonymous_variant 0.4
folC 2746603 c.996C>T synonymous_variant 0.22
folC 2746657 c.942T>A synonymous_variant 0.29
folC 2746808 p.Ala264Val missense_variant 0.29
pepQ 2860374 c.45T>G synonymous_variant 0.2
ribD 2987203 p.Arg122Met missense_variant 0.29
thyX 3067879 p.Val23Leu missense_variant 0.13
Rv3236c 3612051 p.Thr356Ser missense_variant 0.4
Rv3236c 3612134 p.Thr328Ser missense_variant 0.22
Rv3236c 3613184 c.-68C>G upstream_gene_variant 0.67
fbiB 3642262 p.Leu243Pro missense_variant 0.25
fbiB 3642330 p.Phe266Ile missense_variant 0.2
fbiB 3642744 p.Ala404Thr missense_variant 0.25
alr 3841331 p.Gln30His missense_variant 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.27
rpoA 3877735 p.Val258Glu missense_variant 0.23
clpC1 4038776 p.Glu643Asp missense_variant 0.12
clpC1 4039042 p.Ser555Thr missense_variant 0.29
clpC1 4039691 c.1014G>C synonymous_variant 0.22
clpC1 4040144 c.561G>C synonymous_variant 0.14
panD 4043927 p.His119Tyr missense_variant 0.22
embC 4241996 p.Thr712Ala missense_variant 0.4
embA 4242259 c.-974G>T upstream_gene_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242855 p.Gly998Val missense_variant 0.17
embA 4245488 c.2256G>T synonymous_variant 0.25
embB 4246544 p.Thr11Pro missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.71
embB 4246556 p.Ala15Pro missense_variant 0.71
embB 4246584 p.Arg24Pro missense_variant 0.4
embB 4247512 c.999T>C synonymous_variant 0.19
embB 4247516 p.Asn335Asp missense_variant 0.2
embB 4247531 p.Met340Trp missense_variant 0.15
embB 4247534 p.Thr341Ala missense_variant 0.15
embB 4247547 p.Asp345Ala missense_variant 0.15
embB 4247551 c.1038C>A synonymous_variant 0.18
embB 4247555 p.Leu348Ile missense_variant 0.18
ethA 4326024 p.Pro484Ala missense_variant 0.4
ethA 4326069 p.Arg469Trp missense_variant 0.5
ethA 4326754 p.Trp240Cys missense_variant 0.18
ethR 4326811 c.-738G>T upstream_gene_variant 0.22
ethR 4326961 c.-588G>C upstream_gene_variant 0.13
ethR 4326964 c.-585G>A upstream_gene_variant 0.14
ethR 4326970 c.-579G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0