TB-Profiler result

Run: ERR4816133
Summary

Run ID: ERR4816133

Sample name:

Date: 01-04-2023 14:15:23

Number of reads: 1074572

Percentage reads mapped: 80.22

Strain: La1.8.2

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
La1 M.bovis None None 1.0
La1.8 M.bovis None None 1.0
La1.8.2 M.bovis None None 0.99
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 0.65 streptomycin
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide
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 5752 c.513G>A synonymous_variant 1.0
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7162 c.-140C>T upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576000 p.Asp218Gly missense_variant 1.0
rpoB 759950 c.144T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763053 c.-317T>C upstream_gene_variant 0.14
rpoC 763070 c.-300T>C upstream_gene_variant 0.26
rpoB 763077 p.Val1091Thr missense_variant 0.31
rpoC 763082 c.-288C>T upstream_gene_variant 0.12
rpoC 763103 c.-267G>C upstream_gene_variant 0.24
rpoC 763115 c.-255T>C upstream_gene_variant 0.28
rpoB 763119 p.Asn1105Asp missense_variant 0.19
rpoC 763127 c.-243G>C upstream_gene_variant 0.21
rpoC 763133 c.-237G>C upstream_gene_variant 0.15
rpoC 763675 c.306C>G synonymous_variant 0.12
rpoC 763708 c.339G>C synonymous_variant 0.12
rpoC 763714 c.345G>C synonymous_variant 0.12
rpoC 763717 c.348T>C synonymous_variant 0.12
rpoC 763718 p.Leu117Val missense_variant 0.12
rpoC 763723 c.354G>C synonymous_variant 0.13
rpoC 763724 p.Asp119Asn missense_variant 0.13
rpoC 763729 c.360G>C synonymous_variant 0.12
rpoC 763732 c.363C>G synonymous_variant 0.13
rpoC 763735 c.366G>C synonymous_variant 0.13
rpoC 763744 c.375G>C synonymous_variant 0.14
rpoC 763751 p.Ile128Val missense_variant 0.14
rpoC 764559 p.Arg397His missense_variant 0.18
rpoC 764626 c.1257C>T synonymous_variant 0.15
rpoC 764632 c.1263T>C synonymous_variant 0.14
rpoC 764647 c.1278C>T synonymous_variant 0.12
rpoC 764650 c.1281G>T synonymous_variant 0.12
rpoC 764653 c.1284G>C synonymous_variant 0.12
rpoC 764656 c.1287C>G synonymous_variant 0.11
rpoC 764662 c.1293G>C synonymous_variant 0.12
rpoC 764677 c.1308C>G synonymous_variant 0.11
rpoC 764678 p.Lys437Gln missense_variant 0.11
rpoC 765838 c.2469G>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
embR 1416695 p.Ser218Tyr missense_variant 1.0
atpE 1461173 c.129C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.18
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.67
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.46
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.58
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.58
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.59
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.83
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.68
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.68
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.18
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.33
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.81
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.31
rrs 1472274 n.429A>G non_coding_transcript_exon_variant 0.62
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 0.5
rrs 1472338 n.493A>G non_coding_transcript_exon_variant 0.5
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.5
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.6
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.5
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.64
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.72
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.76
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.76
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.2
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.72
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.81
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.68
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.67
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.41
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.22
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 0.57
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.4
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.68
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.18
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.71
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.62
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.63
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.61
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.41
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.56
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.52
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.94
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.3
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.8
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.94
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.25
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.62
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.25
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.96
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.92
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.88
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.73
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.26
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.26
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.97
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.68
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.68
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.94
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.91
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.91
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.89
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.62
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.61
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.65
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.5
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.44
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.44
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.41
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.41
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.47
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.18
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.53
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.32
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.42
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.69
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.77
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.58
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.56
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.11
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.11
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.65
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.86
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.75
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.71
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.71
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.62
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.25
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.36
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.36
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.42
rrl 1473384 n.-274A>G upstream_gene_variant 0.23
rrl 1473425 n.-233G>A upstream_gene_variant 0.12
rrl 1474164 n.507C>T non_coding_transcript_exon_variant 0.5
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.88
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.86
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.88
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.88
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.88
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.12
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.18
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.89
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.21
rrl 1474275 n.618T>C non_coding_transcript_exon_variant 0.67
rrl 1474634 n.977T>C non_coding_transcript_exon_variant 1.0
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 1.0
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 1.0
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 1.0
rrl 1474640 n.983C>T non_coding_transcript_exon_variant 1.0
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 1.0
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.4
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.33
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.5
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.5
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.5
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.5
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.5
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.4
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.4
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.4
rrl 1475995 n.2338G>C non_coding_transcript_exon_variant 0.4
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.4
rrl 1475998 n.2341C>G non_coding_transcript_exon_variant 0.4
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.4
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.5
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.79
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.13
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.76
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.8
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.55
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.74
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.56
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.6
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.75
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.4
rpsA 1833676 c.135A>G synonymous_variant 0.12
rpsA 1833679 c.138G>C synonymous_variant 0.12
rpsA 1833684 p.Arg48His missense_variant 0.12
rpsA 1833694 c.153G>C synonymous_variant 0.22
rpsA 1833700 c.159C>T synonymous_variant 0.21
rpsA 1833721 c.180A>G synonymous_variant 0.29
rpsA 1833724 c.183C>T synonymous_variant 0.25
rpsA 1833727 c.186G>C synonymous_variant 0.25
rpsA 1833732 p.Pro64Leu missense_variant 0.21
rpsA 1833734 p.Ala65Ser missense_variant 0.25
rpsA 1833742 c.201A>G synonymous_variant 0.25
rpsA 1833764 p.Asp75Asn missense_variant 0.33
rpsA 1833770 p.Asn77Asp missense_variant 0.33
rpsA 1833775 p.Glu78Asp missense_variant 0.29
rpsA 1834099 c.558C>T synonymous_variant 0.11
rpsA 1834102 c.561T>C synonymous_variant 0.12
rpsA 1834195 c.654G>C synonymous_variant 0.22
rpsA 1834234 c.693G>C synonymous_variant 0.26
rpsA 1834240 c.699T>C synonymous_variant 0.27
rpsA 1834246 c.705G>T synonymous_variant 0.17
rpsA 1834249 c.708T>C synonymous_variant 0.33
rpsA 1834261 c.720A>G synonymous_variant 0.35
rpsA 1834264 c.723G>C synonymous_variant 0.35
rpsA 1834294 c.753G>C synonymous_variant 0.17
rpsA 1834298 p.Gln253Glu missense_variant 0.17
rpsA 1834306 c.765T>C synonymous_variant 0.14
rpsA 1834307 p.Asp256Gln missense_variant 0.14
rpsA 1834312 c.771G>A synonymous_variant 0.14
rpsA 1834327 c.786G>T synonymous_variant 0.13
rpsA 1834795 c.1254C>T synonymous_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103058 c.-16T>C upstream_gene_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2153966 p.Ala716Ser missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168374 p.Pro747Ser missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222511 c.654C>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
folC 2747631 c.-33C>T upstream_gene_variant 1.0
Rv2752c 3066302 c.-111C>T upstream_gene_variant 0.12
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087871 p.Leu351Arg missense_variant 0.11
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612811 c.306G>A synonymous_variant 0.11
fbiB 3641710 p.Arg59Leu missense_variant 0.12
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4039639 p.Ile356Val missense_variant 0.11
clpC1 4039644 p.His354Pro missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242770 p.Thr970Pro missense_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 0.94
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248372 p.Arg620Pro missense_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
eis 2714045 c.1204_*78delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC stop_lost&conservative_inframe_deletion&splice_region_variant 1.0