TB-Profiler result

Run: ERR2229576
Summary

Run ID: ERR2229576

Sample name:

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

Number of reads: 585788

Percentage reads mapped: 98.99

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 6159 p.Thr307Ile missense_variant 0.17
gyrB 6507 p.Ala423Val missense_variant 0.15
gyrA 6739 c.-563C>A upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 490938 c.156G>T synonymous_variant 0.2
mshA 575442 p.Gly32Val missense_variant 0.4
mshA 575585 p.Ala80Ser missense_variant 0.22
mshA 575644 c.297G>A synonymous_variant 0.18
mshA 576108 p.Ala254Gly missense_variant 0.38
mshA 576641 p.Asn432Asp missense_variant 0.14
ccsA 620722 c.833delA frameshift_variant 0.14
rpoB 760228 p.Ile141Asn missense_variant 0.25
rpoB 760358 c.552C>A synonymous_variant 0.17
rpoB 762130 p.Leu775His missense_variant 0.13
rpoB 763057 p.Thr1084Asn missense_variant 0.4
rpoC 763709 p.Leu114Met missense_variant 0.12
rpoC 763742 p.Leu125Met missense_variant 0.12
rpoC 765121 c.1752G>T synonymous_variant 0.18
rpoC 765473 p.Glu702* stop_gained 0.29
rpoC 765651 p.Gln761Arg missense_variant 0.33
rpoC 765822 p.Ala818Asp missense_variant 0.29
rpoC 766303 p.Cys978* stop_gained 0.18
rpoC 766501 c.3132G>T synonymous_variant 0.5
rpoC 766759 c.3390G>T synonymous_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777187 p.Ala432Ser missense_variant 0.15
mmpL5 778440 p.Pro14Gln missense_variant 0.12
mmpR5 779131 p.Pro48Thr missense_variant 0.29
mmpS5 779559 c.-654G>T upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781850 c.291C>A synonymous_variant 0.18
fbiC 1302748 c.-183C>A upstream_gene_variant 0.33
fbiC 1302786 c.-145C>A upstream_gene_variant 0.2
fbiC 1302837 c.-94G>A upstream_gene_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304429 p.Arg500Leu missense_variant 0.22
fbiC 1304682 c.1752C>T synonymous_variant 0.13
fbiC 1305303 c.2373T>C synonymous_variant 0.11
Rv1258c 1406985 p.Ala119Glu missense_variant 0.12
Rv1258c 1407007 p.Leu112Met missense_variant 0.13
Rv1258c 1407332 p.Asn3Lys missense_variant 0.2
atpE 1461111 p.Gly23Ser missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472196 n.351C>A non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474239 n.582G>T non_coding_transcript_exon_variant 0.13
rrl 1475156 n.1499G>T non_coding_transcript_exon_variant 0.4
fabG1 1673180 c.-260C>T upstream_gene_variant 0.22
fabG1 1673346 c.-94C>G upstream_gene_variant 0.13
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
rpsA 1834104 p.Arg188His missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102390 p.Pro218Gln missense_variant 0.4
katG 2155769 p.Ile115Leu missense_variant 0.2
katG 2156182 c.-71T>C upstream_gene_variant 0.22
PPE35 2167814 c.2799C>T synonymous_variant 0.17
PPE35 2168475 p.Pro713His missense_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169302 p.Met437Ile missense_variant 0.12
PPE35 2169662 c.951T>C synonymous_variant 0.18
PPE35 2169666 p.Asn316Thr missense_variant 0.18
PPE35 2169902 p.Leu237Phe missense_variant 0.27
PPE35 2170048 p.Leu189Val missense_variant 0.68
PPE35 2170053 p.Thr187Ser missense_variant 0.63
PPE35 2170147 p.Ser156Ala missense_variant 0.21
PPE35 2170557 c.55delG frameshift_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289124 p.Asp40Asn missense_variant 0.15
pncA 2289312 c.-71G>T upstream_gene_variant 0.2
pncA 2289813 c.-572G>A upstream_gene_variant 0.29
kasA 2518197 p.Asp28Ala missense_variant 0.13
kasA 2519122 c.1008G>A synonymous_variant 0.17
kasA 2519131 c.1017G>C synonymous_variant 0.14
kasA 2519181 p.Val356Gly missense_variant 0.12
eis 2714853 c.480C>T synonymous_variant 0.5
ahpC 2726253 p.Gly21Ser missense_variant 0.12
folC 2747280 p.Arg107Ser missense_variant 0.2
pepQ 2860277 p.Asp48Asn missense_variant 0.18
Rv2752c 3065275 p.Gly306Val missense_variant 0.18
Rv2752c 3065289 c.903G>T synonymous_variant 0.2
Rv2752c 3065536 p.Gly219Asp missense_variant 0.29
Rv2752c 3066375 c.-184G>A upstream_gene_variant 0.2
Rv2752c 3067000 c.-809T>A upstream_gene_variant 0.2
Rv2752c 3067055 c.-865delT upstream_gene_variant 0.17
thyX 3068041 c.-96C>A upstream_gene_variant 0.25
ald 3087049 p.Pro77Gln missense_variant 0.18
ald 3087575 c.756T>C synonymous_variant 0.25
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474232 p.Phe76Leu missense_variant 0.25
fprA 3474621 c.615C>A synonymous_variant 0.2
whiB7 3568817 c.-138C>A upstream_gene_variant 0.2
Rv3236c 3612994 c.123G>A synonymous_variant 0.5
fbiA 3640562 p.Ala7Asp missense_variant 0.18
fbiB 3642441 p.Pro303Thr missense_variant 0.15
fbiB 3642658 p.Val375Gly missense_variant 0.22
fbiB 3642676 p.Val381Gly missense_variant 0.2
alr 3840525 p.Trp299Leu missense_variant 0.25
alr 3840558 p.Arg288His missense_variant 0.22
alr 3840975 p.Gly149Asp missense_variant 0.18
alr 3841434 c.-14C>T upstream_gene_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.29
alr 3841612 c.-193_-192insC upstream_gene_variant 0.15
rpoA 3877563 p.Phe315Leu missense_variant 0.12
rpoA 3877874 p.Gly212Cys missense_variant 0.4
clpC1 4039003 p.Asn568Asp missense_variant 0.17
clpC1 4039018 p.Ser563Ala missense_variant 0.21
clpC1 4039022 c.1683A>G synonymous_variant 0.21
clpC1 4039031 c.1674T>C synonymous_variant 0.16
clpC1 4039161 p.His515Gly missense_variant 0.23
clpC1 4039169 p.Glu512Asp missense_variant 0.21
clpC1 4039339 p.Thr456Ser missense_variant 1.0
clpC1 4039605 p.Glu367Val missense_variant 0.18
clpC1 4039713 p.Tyr331Phe missense_variant 0.18
clpC1 4039916 c.789T>C synonymous_variant 0.18
clpC1 4040144 c.561G>C synonymous_variant 0.43
clpC1 4040233 p.Arg158Ser missense_variant 0.33
clpC1 4040360 p.Glu115Asp missense_variant 0.2
embC 4241506 c.1644G>A synonymous_variant 0.25
embC 4241756 p.Leu632Met missense_variant 0.29
embA 4242289 c.-944C>T upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244237 p.Cys335* stop_gained 0.12
embA 4244666 c.1434G>C synonymous_variant 0.17
embA 4245434 c.2202G>T synonymous_variant 0.17
embB 4246208 c.-306G>T upstream_gene_variant 0.4
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.64
embB 4246555 c.42G>C synonymous_variant 0.6
embB 4246556 p.Ala15Pro missense_variant 0.6
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.33
aftB 4267390 p.Gln483Lys missense_variant 0.13
ethA 4326383 p.Thr364Ile missense_variant 0.22
ethA 4327262 p.Gly71Val missense_variant 0.15
ethR 4328068 p.Ala174Ser missense_variant 0.25
ethA 4328413 c.-940C>A upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407625 p.Ala193Val missense_variant 0.29
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0