TB-Profiler result

Run: ERR1750909
Summary

Run ID: ERR1750909

Sample name:

Date: 31-03-2023 14:59:19

Number of reads: 1447232

Percentage reads mapped: 87.07

Strain: lineage4.1.1.2

Drug-resistance: RR-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 1.0
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.99
lineage4.1.1.2 Euro-American (X-type) X1 None 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
rpoB 761135 p.Leu443Phe missense_variant 0.12 rifampicin
rrs 1472272 n.427G>C non_coding_transcript_exon_variant 0.11 streptomycin
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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760223 c.417T>C synonymous_variant 0.12
rpoB 760234 p.Ser143Thr missense_variant 0.12
rpoB 760241 c.435G>C synonymous_variant 0.13
rpoB 760244 c.438G>C synonymous_variant 0.13
rpoB 760253 c.447T>C synonymous_variant 0.13
rpoB 760265 p.Met153Ile missense_variant 0.12
rpoB 761150 c.1344A>C synonymous_variant 0.12
rpoB 761165 c.1359G>C synonymous_variant 0.11
rpoB 761189 c.1383T>C synonymous_variant 0.12
rpoB 761195 c.1389G>C synonymous_variant 0.15
rpoB 761196 p.Leu464Val missense_variant 0.15
rpoC 763007 c.-363C>T upstream_gene_variant 0.16
rpoC 764683 c.1314G>C synonymous_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777036 p.Gln482Arg missense_variant 0.12
mmpS5 778704 p.Asn68Asp missense_variant 0.12
mmpL5 778951 c.-471G>T upstream_gene_variant 0.2
mmpS5 779644 c.-739G>T upstream_gene_variant 0.21
mmpS5 779687 c.-782C>G upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781533 c.-27A>G upstream_gene_variant 0.14
rplC 800813 p.Ala2Gly missense_variant 0.15
embR 1417141 c.207C>T synonymous_variant 0.15
embR 1417157 p.Pro64Arg missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471916 n.71G>C non_coding_transcript_exon_variant 0.12
rrs 1471952 n.107G>T non_coding_transcript_exon_variant 0.22
rrs 1471985 n.141_142delCG non_coding_transcript_exon_variant 0.33
rrs 1472078 n.233C>A non_coding_transcript_exon_variant 0.2
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.25
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.43
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.29
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.5
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.38
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.18
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.14
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.31
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.44
rrs 1472256 n.411T>C non_coding_transcript_exon_variant 0.21
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.17
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.5
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.22
rrs 1472671 n.826G>T non_coding_transcript_exon_variant 0.22
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.15
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.15
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.18
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.29
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.22
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.25
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.25
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.25
rrs 1472997 n.1152G>T non_coding_transcript_exon_variant 0.29
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.18
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.18
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.25
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.23
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.21
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.2
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.2
rrs 1473112 n.1267A>G non_coding_transcript_exon_variant 0.12
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.2
rrs 1473134 n.1289T>C non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.44
rrl 1473746 n.89T>A non_coding_transcript_exon_variant 0.33
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.29
rrl 1473811 n.154C>A non_coding_transcript_exon_variant 0.29
rrl 1473812 n.155G>C non_coding_transcript_exon_variant 0.29
rrl 1473815 n.158T>G non_coding_transcript_exon_variant 0.25
rrl 1473822 n.165A>G non_coding_transcript_exon_variant 0.22
rrl 1473828 n.171_172insCT non_coding_transcript_exon_variant 0.25
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 0.22
rrl 1473836 n.179delA non_coding_transcript_exon_variant 0.25
rrl 1473844 n.187C>T non_coding_transcript_exon_variant 0.27
rrl 1473854 n.197A>G non_coding_transcript_exon_variant 0.2
rrl 1473870 n.213G>A non_coding_transcript_exon_variant 0.17
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.15
rrl 1473909 n.252G>A non_coding_transcript_exon_variant 0.15
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.5
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.5
rrl 1474202 n.545T>A non_coding_transcript_exon_variant 0.5
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.5
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.29
rrl 1474351 n.694G>C non_coding_transcript_exon_variant 0.21
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.25
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.27
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.27
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.21
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.23
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.29
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.25
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.23
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.21
rrl 1474688 n.1031G>T non_coding_transcript_exon_variant 0.33
rrl 1474720 n.1063C>T non_coding_transcript_exon_variant 0.25
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.22
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.15
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.18
rrl 1475621 n.1964T>G non_coding_transcript_exon_variant 0.14
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.15
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.12
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.2
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.13
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.12
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.2
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.21
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.11
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.24
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.2
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.31
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.25
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.3
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.23
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476272 n.2615A>C non_coding_transcript_exon_variant 0.12
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.23
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.24
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.26
rrl 1476300 n.2643G>A non_coding_transcript_exon_variant 0.2
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.24
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.15
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.15
rrl 1476371 n.2714A>C non_coding_transcript_exon_variant 0.12
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>A non_coding_transcript_exon_variant 0.17
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.42
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.36
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.22
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.22
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.18
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.18
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.3
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.22
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.18
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.29
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.29
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.29
rrl 1476661 n.3004A>G non_coding_transcript_exon_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 0.97
ndh 2101911 p.Ala378Thr missense_variant 0.15
ndh 2102141 p.Gly301Val missense_variant 0.16
katG 2154072 c.2040C>A synonymous_variant 0.29
katG 2155296 c.816C>T synonymous_variant 1.0
katG 2155741 p.Gly124Asp missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518367 p.Arg85Gly missense_variant 0.15
kasA 2518420 p.Glu102Asp missense_variant 0.15
kasA 2518856 p.Ile248Val missense_variant 0.12
eis 2715280 p.Leu18Pro missense_variant 0.12
pepQ 2859344 p.Pro359Ser missense_variant 0.18
pepQ 2859793 p.Asp209Val missense_variant 0.18
pepQ 2860355 p.Met22Val missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339176 p.Ala20Gly missense_variant 0.13
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.17
Rv3083 3449787 c.1284C>T synonymous_variant 1.0
fprA 3473855 c.-152G>A upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474182 p.Lys59Arg missense_variant 0.11
fprA 3474975 c.969C>A synonymous_variant 0.15
whiB7 3568713 c.-34C>T upstream_gene_variant 0.14
whiB7 3568720 c.-41C>G upstream_gene_variant 0.13
Rv3236c 3611998 c.1119C>G synonymous_variant 0.12
rpoA 3877613 p.Ile299Val missense_variant 0.12
rpoA 3877617 c.891G>C synonymous_variant 0.12
rpoA 3877629 c.879C>G synonymous_variant 0.11
rpoA 3878316 c.192C>A synonymous_variant 0.22
rpoA 3878641 c.-135delG upstream_gene_variant 0.67
rpoA 3878684 c.-177T>A upstream_gene_variant 0.2
clpC1 4038551 c.2154C>G synonymous_variant 0.14
clpC1 4038556 p.Ile717Val missense_variant 0.18
clpC1 4038584 c.2121G>C synonymous_variant 0.19
clpC1 4038587 c.2118C>G synonymous_variant 0.15
clpC1 4038596 c.2109A>G synonymous_variant 0.11
clpC1 4038623 c.2082A>G synonymous_variant 0.12
clpC1 4038702 p.Leu668Pro missense_variant 0.11
clpC1 4038859 p.Arg616Ser missense_variant 0.17
clpC1 4039161 p.His515Arg missense_variant 0.11
clpC1 4039676 c.1029G>A synonymous_variant 1.0
clpC1 4039864 p.Asp281His missense_variant 0.12
clpC1 4039882 c.811_822delAAGGTGCTCAAG conservative_inframe_deletion 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.97
embC 4243015 p.Asp1051Glu missense_variant 0.17
embA 4243833 p.Ala201Thr missense_variant 0.97
embB 4246835 p.Asp108Tyr missense_variant 0.18
embB 4246930 p.Gln139His missense_variant 1.0
embB 4246942 c.429G>A synonymous_variant 0.2
embB 4249062 p.Thr850Ile missense_variant 0.2
embB 4249408 c.2895G>A synonymous_variant 1.0
ethA 4326487 c.987A>G synonymous_variant 0.12
ethR 4327672 p.Leu42Met missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0