TB-Profiler result

Run: ERR4815811
Summary

Run ID: ERR4815811

Sample name:

Date: 01-04-2023 14:04:40

Number of reads: 636411

Percentage reads mapped: 53.87

Strain: lineage4.2.1.1

Drug-resistance: HR-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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.67 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288957 p.Tyr95* stop_gained 1.0 pyrazinamide
ethA 4327409 p.His22Pro missense_variant 1.0 ethionamide
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 490682 c.-101C>T upstream_gene_variant 0.11
mshA 575833 c.486C>T synonymous_variant 1.0
mshA 576092 p.Pro249Ala missense_variant 1.0
rpoB 761884 p.Gly693Ala missense_variant 0.11
rpoB 762009 p.Leu735Val missense_variant 0.11
rpoB 762024 p.Val740Ile missense_variant 0.17
rpoB 762029 c.2223C>G synonymous_variant 0.17
rpoB 762051 p.His749Tyr missense_variant 0.22
rpoB 762057 p.Ile751Val missense_variant 0.18
rpoB 762062 c.2256T>C synonymous_variant 0.17
rpoB 762065 c.2259T>C synonymous_variant 0.17
rpoB 762071 p.Asp755Glu missense_variant 0.17
rpoB 762080 c.2274G>C synonymous_variant 0.17
rpoB 762085 p.Ala760Glu missense_variant 0.18
rpoB 762089 c.2283G>A synonymous_variant 0.17
rpoB 762194 c.2388G>C synonymous_variant 0.17
rpoB 762200 c.2394C>T synonymous_variant 0.19
rpoB 762212 c.2406G>C synonymous_variant 0.14
rpoB 762218 c.2412T>C synonymous_variant 0.15
rpoB 762233 c.2427G>C synonymous_variant 0.16
rpoB 762234 p.Pro810Ser missense_variant 0.16
rpoB 762239 c.2433G>A synonymous_variant 0.16
rpoB 762245 c.2439G>C synonymous_variant 0.18
rpoB 762254 c.2448T>C synonymous_variant 0.18
rpoB 762293 c.2487T>C synonymous_variant 0.13
rpoC 762929 c.-441G>C upstream_gene_variant 0.11
rpoB 763038 p.Thr1078Ala missense_variant 0.17
rpoC 763043 c.-327G>C upstream_gene_variant 0.33
rpoC 763053 c.-317T>C upstream_gene_variant 0.46
rpoC 763070 c.-300T>C upstream_gene_variant 0.47
rpoB 763077 p.Val1091Ser missense_variant 0.5
rpoC 763103 c.-267G>C upstream_gene_variant 0.5
rpoC 763115 c.-255T>C upstream_gene_variant 0.44
rpoB 763119 p.Asn1105Asp missense_variant 0.44
rpoC 763127 c.-243G>C upstream_gene_variant 0.5
rpoC 763133 c.-237G>C upstream_gene_variant 0.36
rpoC 763148 c.-222G>C upstream_gene_variant 0.22
rpoC 763570 c.201G>C synonymous_variant 0.2
rpoC 763578 p.Phe70Tyr missense_variant 0.2
rpoC 764503 c.1134G>T synonymous_variant 0.17
rpoC 764512 c.1143G>C synonymous_variant 0.12
rpoC 764521 c.1152T>C synonymous_variant 0.12
rpoC 764530 c.1161C>T synonymous_variant 0.14
rpoC 764543 p.Thr392Ala missense_variant 0.21
rpoC 764548 c.1179G>C synonymous_variant 0.21
rpoC 764573 p.Leu402Ile missense_variant 0.14
rpoC 764578 c.1209C>G synonymous_variant 0.15
rpoC 764581 c.1212T>C synonymous_variant 0.15
rpoC 764582 p.Leu405Met missense_variant 0.14
rpoC 764593 c.1224C>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 1.0
mmpL5 779475 c.-995T>A upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800973 c.165C>T synonymous_variant 1.0
Rv1258c 1407494 c.-154A>G upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471755 n.-91C>T upstream_gene_variant 1.0
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.4
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.5
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.87
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.91
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.91
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.94
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.91
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.9
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.92
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.95
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.97
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.58
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.95
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 0.5
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.62
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.7
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.7
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.78
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.82
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.16
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.76
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.76
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.72
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.84
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.94
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.24
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.73
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.73
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.66
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.6
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.8
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.29
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.57
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.29
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.29
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.67
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.67
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.7
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.18
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.7
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.22
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.7
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.62
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.62
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.58
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.33
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.58
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.57
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.73
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.36
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.29
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.71
rrs 1472840 n.995A>G non_coding_transcript_exon_variant 0.43
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.68
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.84
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.84
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.84
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.86
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.7
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.92
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.89
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.88
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.83
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.88
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.94
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.89
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.61
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.87
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.91
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.91
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 1.0
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.88
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.92
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.93
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 1.0
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.89
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 1.0
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.69
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.94
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.95
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.86
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.86
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.77
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.93
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.88
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.9
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.9
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.6
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.21
rrs 1473291 n.1446G>C non_coding_transcript_exon_variant 0.82
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.86
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.86
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.86
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.92
rrl 1474164 n.507C>T non_coding_transcript_exon_variant 1.0
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.92
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.92
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.92
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.92
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.92
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.81
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.67
rrl 1474896 n.1239A>T non_coding_transcript_exon_variant 0.67
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 0.67
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.67
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.67
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.67
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.67
rrl 1474938 n.1281G>A non_coding_transcript_exon_variant 0.67
rrl 1474945 n.1288C>A non_coding_transcript_exon_variant 0.67
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.67
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 1.0
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 1.0
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.9
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.91
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.95
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.94
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 1.0
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.78
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.71
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.67
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.5
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.5
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.5
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.5
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.5
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.5
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.5
rrl 1476548 n.2891T>C non_coding_transcript_exon_variant 0.4
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.38
rrl 1476573 n.2916A>G non_coding_transcript_exon_variant 0.29
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.67
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.83
rrl 1476594 n.2937C>A non_coding_transcript_exon_variant 0.83
rrl 1476603 n.2946G>T non_coding_transcript_exon_variant 0.83
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.67
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.67
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.83
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.67
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.71
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.67
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.57
rrl 1476661 n.3004A>G non_coding_transcript_exon_variant 0.33
rpsA 1834234 c.693G>C synonymous_variant 0.37
rpsA 1834240 c.699T>C synonymous_variant 0.32
rpsA 1834249 c.708T>C synonymous_variant 0.39
rpsA 1834261 c.720A>G synonymous_variant 0.37
rpsA 1834264 c.723G>C synonymous_variant 0.37
rpsA 1834294 c.753G>C synonymous_variant 0.4
rpsA 1834298 p.Gln253Glu missense_variant 0.4
rpsA 1834306 c.765T>C synonymous_variant 0.37
rpsA 1834307 p.Asp256Gln missense_variant 0.37
rpsA 1834312 c.771G>A synonymous_variant 0.39
rpsA 1834327 c.786G>T synonymous_variant 0.31
rpsA 1834345 c.804C>T synonymous_variant 0.2
rpsA 1834348 c.807T>C synonymous_variant 0.2
rpsA 1834354 c.813G>C synonymous_variant 0.17
rpsA 1834366 c.825A>C synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289796 c.-555T>A upstream_gene_variant 0.33
ahpC 2726250 p.Gly20Ser missense_variant 0.29
ald 3086742 c.-78A>C upstream_gene_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449132 p.Leu210Arg missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3987092 p.Glu83Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246587 p.Gly25Ala missense_variant 1.0
embB 4247223 p.Trp237Ser missense_variant 0.11
embB 4247790 p.Ser426Asn missense_variant 1.0
whiB6 4338460 p.Met21Thr missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407969 c.233dupC frameshift_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0