TB-Profiler result

Run: ERR4820265
Summary

Run ID: ERR4820265

Sample name:

Date: 01-04-2023 16:34:54

Number of reads: 1275382

Percentage reads mapped: 79.02

Strain: lineage4.1.2.1

Drug-resistance: Other

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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 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.75 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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762185 c.2379G>C synonymous_variant 0.11
rpoB 762194 c.2388G>C synonymous_variant 0.21
rpoB 762200 c.2394C>T synonymous_variant 0.23
rpoB 762218 c.2412T>C synonymous_variant 0.23
rpoB 762233 c.2427G>C synonymous_variant 0.24
rpoB 762234 p.Pro810Ser missense_variant 0.24
rpoB 762245 c.2439G>C synonymous_variant 0.23
rpoB 762254 c.2448T>C synonymous_variant 0.22
rpoC 763043 c.-327G>C upstream_gene_variant 0.24
rpoC 763053 c.-317T>C upstream_gene_variant 0.35
rpoC 763067 c.-303C>G upstream_gene_variant 0.32
rpoC 763070 c.-300T>C upstream_gene_variant 0.32
rpoB 763077 p.Val1091Thr missense_variant 0.3
rpoC 763103 c.-267G>C upstream_gene_variant 0.25
rpoC 763109 c.-261C>T upstream_gene_variant 0.22
rpoC 763115 c.-255T>C upstream_gene_variant 0.19
rpoB 763119 p.Asn1105Asp missense_variant 0.19
rpoC 763127 c.-243G>C upstream_gene_variant 0.13
rpoC 763133 c.-237G>C upstream_gene_variant 0.12
rpoC 763675 c.306C>G synonymous_variant 0.17
rpoC 763699 c.330G>T synonymous_variant 0.18
rpoC 763708 c.339G>C synonymous_variant 0.19
rpoC 763714 c.345G>C synonymous_variant 0.16
rpoC 763717 c.348T>C synonymous_variant 0.12
rpoC 763718 p.Leu117Val missense_variant 0.12
rpoC 763723 c.354G>C synonymous_variant 0.12
rpoC 763724 p.Asp119Asn missense_variant 0.12
rpoC 763729 c.360G>C synonymous_variant 0.12
rpoC 763732 c.363C>G synonymous_variant 0.11
rpoC 763735 c.366G>C synonymous_variant 0.11
rpoC 763744 c.375G>C synonymous_variant 0.12
rpoC 763751 p.Ile128Val missense_variant 0.12
rpoC 764015 c.646C>T synonymous_variant 0.12
rpoC 764632 c.1263T>C synonymous_variant 0.13
rpoC 764647 c.1278C>T synonymous_variant 0.11
rpoC 764650 c.1281G>T synonymous_variant 0.13
rpoC 764653 c.1284G>C synonymous_variant 0.11
rpoC 764662 c.1293G>C synonymous_variant 0.1
rpoC 764677 c.1308C>G synonymous_variant 0.17
rpoC 764678 p.Lys437Gln missense_variant 0.17
rpoC 764692 c.1323C>T synonymous_variant 0.17
rpoC 764706 p.Leu446Gln missense_variant 0.21
rpoC 764731 c.1362G>C synonymous_variant 0.14
rpoC 764780 p.Ser471Ala missense_variant 0.12
rpoC 764793 p.Met475Lys missense_variant 0.12
rpoC 764797 c.1428G>T synonymous_variant 0.11
rpoC 764803 c.1434C>T synonymous_variant 0.11
rpoC 764813 p.Gln482Glu missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766551 p.Phe1061Tyr missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417068 c.280T>C synonymous_variant 0.12
embR 1417402 c.-55A>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472068 n.223T>G non_coding_transcript_exon_variant 0.29
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.29
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.33
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.15
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.4
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.36
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.36
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.36
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.13
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.13
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.13
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.13
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.64
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.14
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.41
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.41
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.33
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.56
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.94
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 1.0
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 1.0
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 1.0
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 1.0
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.75
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.8
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.8
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.82
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.86
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.91
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.94
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.88
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.93
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.32
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.98
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.95
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.95
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.54
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.67
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.21
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.8
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.3
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.72
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.73
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.73
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.74
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.24
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.71
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.69
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.89
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.27
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.45
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.82
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.67
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.85
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.92
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.92
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.93
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 1.0
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.91
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.88
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 1.0
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 1.0
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 1.0
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.4
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.4
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.67
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.5
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.6
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.6
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.6
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.33
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.41
rrs 1473122 n.1281delA non_coding_transcript_exon_variant 0.46
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.73
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.72
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.48
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.59
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.54
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.67
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.75
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.12
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.82
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.67
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.17
rrs 1473293 n.1449delA non_coding_transcript_exon_variant 0.5
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.58
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.7
rrs 1473314 n.1469A>G non_coding_transcript_exon_variant 0.15
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.64
rrl 1473384 n.-274A>G upstream_gene_variant 0.25
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.67
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.57
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.71
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.67
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.67
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.8
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.25
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.83
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.33
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 1.0
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 1.0
rrl 1474355 n.698A>G non_coding_transcript_exon_variant 1.0
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 1.0
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 1.0
rrl 1474393 n.736A>G non_coding_transcript_exon_variant 1.0
rrl 1474402 n.745T>C non_coding_transcript_exon_variant 1.0
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 1.0
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 1.0
rrl 1474732 n.1075A>T non_coding_transcript_exon_variant 0.5
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 1.0
rrl 1474734 n.1077G>C non_coding_transcript_exon_variant 1.0
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.4
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.5
rrl 1474783 n.1126G>T non_coding_transcript_exon_variant 0.5
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.33
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.6
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.8
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.6
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.67
rrl 1475672 n.2015C>T non_coding_transcript_exon_variant 0.67
rrl 1475694 n.2038_2039insACG non_coding_transcript_exon_variant 0.67
rrl 1475697 n.2040C>T non_coding_transcript_exon_variant 0.5
rrl 1475703 n.2046A>T non_coding_transcript_exon_variant 0.5
rrl 1475707 n.2050T>G non_coding_transcript_exon_variant 0.5
rrl 1475785 n.2128A>G non_coding_transcript_exon_variant 0.4
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.67
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.33
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.57
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.57
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.92
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.9
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.73
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.43
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.27
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.2
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.21
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.17
rrl 1476535 n.2878G>A non_coding_transcript_exon_variant 0.33
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.5
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.5
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.33
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.33
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.5
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.5
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.5
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.5
inhA 1674356 p.Asp52Gly missense_variant 0.12
rpsA 1833727 c.186G>C synonymous_variant 0.14
rpsA 1833732 p.Pro64Leu missense_variant 0.14
rpsA 1833736 c.195C>T synonymous_variant 0.14
rpsA 1833742 c.201A>G synonymous_variant 0.14
rpsA 1834186 c.645C>G synonymous_variant 0.11
rpsA 1834189 c.648G>T synonymous_variant 0.1
rpsA 1834195 c.654G>C synonymous_variant 0.15
rpsA 1834228 c.687C>T synonymous_variant 0.15
rpsA 1834240 c.699T>C synonymous_variant 0.16
rpsA 1834246 c.705G>T synonymous_variant 0.16
rpsA 1834249 c.708T>C synonymous_variant 0.18
rpsA 1834261 c.720A>G synonymous_variant 0.27
rpsA 1834264 c.723G>C synonymous_variant 0.28
rpsA 1834294 c.753G>T synonymous_variant 0.21
rpsA 1834298 p.Gln253Glu missense_variant 0.21
rpsA 1834306 c.765T>C synonymous_variant 0.19
rpsA 1834307 p.Asp256Gln missense_variant 0.16
rpsA 1834312 c.771G>A synonymous_variant 0.14
rpsA 1834327 c.786G>T synonymous_variant 0.14
rpsA 1834345 c.804C>T synonymous_variant 0.12
rpsA 1834348 c.807T>C synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155272 c.840G>A synonymous_variant 0.17
PPE35 2168163 p.Pro817Leu missense_variant 0.11
Rv1979c 2222127 c.1038C>T synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2746704 p.Ala299Ser missense_variant 0.12
folC 2747702 c.-104T>C upstream_gene_variant 0.1
Rv2752c 3065424 c.768C>T synonymous_variant 0.14
Rv2752c 3065535 c.656delG frameshift_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474081 c.75C>G synonymous_variant 0.1
Rv3236c 3612926 c.190delA frameshift_variant 0.11
fbiA 3640363 c.-180C>G upstream_gene_variant 0.11
clpC1 4039098 p.Arg536Pro missense_variant 0.1
clpC1 4039724 c.981A>G synonymous_variant 0.12
clpC1 4039751 c.954A>G synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0