TB-Profiler result

Run: ERR4814356
Summary

Run ID: ERR4814356

Sample name:

Date: 01-04-2023 13:14:53

Number of reads: 414584

Percentage reads mapped: 66.83

Strain: lineage3.1.2

Drug-resistance: Pre-XDR-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
lineage3 East-African-Indian CAS RD750 0.99
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 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
gyrB 6620 p.Asp461Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.44 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762926 c.-444C>G upstream_gene_variant 0.12
rpoC 762929 c.-441G>C upstream_gene_variant 0.12
rpoC 762971 c.-399G>C upstream_gene_variant 0.12
rpoC 762989 c.-381G>C upstream_gene_variant 0.18
rpoC 762995 c.-375G>C upstream_gene_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763038 p.Thr1078Ala missense_variant 0.17
rpoC 763043 c.-327G>C upstream_gene_variant 0.18
rpoC 763050 c.-320C>T upstream_gene_variant 0.18
rpoC 763053 c.-317T>C upstream_gene_variant 0.2
rpoC 763070 c.-300T>C upstream_gene_variant 0.2
rpoB 763077 p.Val1091Ser missense_variant 0.2
rpoC 763103 c.-267G>C upstream_gene_variant 0.22
rpoC 763115 c.-255T>C upstream_gene_variant 0.29
rpoB 763119 p.Asn1105Asp missense_variant 0.29
rpoC 763127 c.-243G>C upstream_gene_variant 0.4
rpoC 763492 c.123G>C synonymous_variant 0.4
rpoC 763528 c.159G>C synonymous_variant 0.4
rpoC 763531 c.162G>C synonymous_variant 0.4
rpoC 763534 c.165T>C synonymous_variant 0.4
rpoC 763675 c.306C>G synonymous_variant 0.23
rpoC 763699 c.330G>T synonymous_variant 0.27
rpoC 763702 c.333C>T synonymous_variant 0.18
rpoC 763708 c.339G>C synonymous_variant 0.36
rpoC 763714 c.345G>C synonymous_variant 0.25
rpoC 763717 c.348T>C synonymous_variant 0.27
rpoC 763718 p.Leu117Val missense_variant 0.27
rpoC 763723 c.354G>C synonymous_variant 0.27
rpoC 763724 p.Asp119Asn missense_variant 0.27
rpoC 763729 c.360G>C synonymous_variant 0.27
rpoC 763732 c.363C>G synonymous_variant 0.27
rpoC 763735 c.366G>C synonymous_variant 0.33
rpoC 763744 c.375G>C synonymous_variant 0.3
rpoC 763751 p.Ile128Val missense_variant 0.3
rpoC 763772 p.Val135Met missense_variant 0.22
rpoC 764246 p.Leu293Ile missense_variant 1.0
rpoC 764461 c.1092A>G synonymous_variant 0.33
rpoC 764485 c.1116G>C synonymous_variant 0.38
rpoC 764491 c.1122G>T synonymous_variant 0.38
rpoC 764497 c.1128A>G synonymous_variant 0.29
rpoC 764503 c.1134G>T synonymous_variant 0.43
rpoC 764512 c.1143G>C synonymous_variant 0.38
rpoC 764521 c.1152T>C synonymous_variant 0.38
rpoC 764530 c.1161C>T synonymous_variant 0.38
rpoC 764536 c.1167G>C synonymous_variant 0.29
rpoC 764611 c.1242G>T synonymous_variant 0.18
rpoC 764632 c.1263T>A synonymous_variant 0.23
rpoC 764634 p.Val422Ala missense_variant 0.15
rpoC 764647 c.1278C>T synonymous_variant 0.17
rpoC 764650 c.1281G>T synonymous_variant 0.15
rpoC 764653 c.1284G>C synonymous_variant 0.15
rpoC 764662 c.1293G>C synonymous_variant 0.18
rpoC 764677 c.1308C>G synonymous_variant 0.18
rpoC 764678 p.Lys437Gln missense_variant 0.18
rpoC 764683 c.1314G>C synonymous_variant 0.18
rpoC 764692 c.1323C>T synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776482 p.Ala667Ser missense_variant 0.2
mmpL5 776585 c.1896C>T synonymous_variant 1.0
mmpS5 778477 c.429A>G stop_lost&splice_region_variant 1.0
mmpR5 779311 p.Ile108Val missense_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781748 c.189C>G synonymous_variant 0.33
rpsL 781751 c.192G>C synonymous_variant 0.33
rpsL 781760 c.201T>C synonymous_variant 0.29
rpsL 781766 c.207C>T synonymous_variant 0.25
rpsL 781796 p.Met79Ile missense_variant 0.25
rpsL 781802 c.243G>C synonymous_variant 0.2
rpsL 781805 c.246G>T synonymous_variant 0.2
rpsL 781811 c.252C>T synonymous_variant 0.18
rpsL 781814 c.255C>T synonymous_variant 0.18
rpsL 781817 c.258G>T synonymous_variant 0.18
rpsL 781832 c.273T>C synonymous_variant 0.2
rpsL 781835 c.276T>C synonymous_variant 0.22
fbiC 1303556 p.Pro209Leu missense_variant 0.29
Rv1258c 1406242 p.Ala367Thr missense_variant 1.0
embR 1416235 c.1113C>A synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472068 n.223T>G non_coding_transcript_exon_variant 0.5
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.5
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.67
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 1.0
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.85
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.92
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.92
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.82
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.83
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.19
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.83
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.12
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.12
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.12
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.83
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.91
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.4
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.5
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.43
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.43
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.43
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.47
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.45
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.45
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.52
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.4
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.41
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.31
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 0.62
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.37
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.37
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.69
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.44
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.56
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.44
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.5
rrs 1472673 n.828T>A non_coding_transcript_exon_variant 1.0
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 1.0
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.75
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 1.0
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.75
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.6
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.4
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.55
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.45
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.58
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.44
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.43
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.12
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.43
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.54
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.44
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.42
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.57
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1472840 n.995A>G non_coding_transcript_exon_variant 1.0
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 1.0
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 1.0
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 1.0
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 1.0
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 1.0
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 1.0
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 1.0
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.96
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.93
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.93
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.93
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.93
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.85
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.85
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 1.0
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 1.0
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 1.0
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.88
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 1.0
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 1.0
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 1.0
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.79
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.91
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.95
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.95
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.95
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.95
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.95
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.95
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.94
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.94
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.91
rrs 1473289 n.1444_1445insTTTTG non_coding_transcript_exon_variant 1.0
rrs 1473293 n.1449delA non_coding_transcript_exon_variant 1.0
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 1.0
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 1.0
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 1.0
rrl 1474163 n.506C>T non_coding_transcript_exon_variant 1.0
rrl 1474164 n.507C>T non_coding_transcript_exon_variant 1.0
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 1.0
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 1.0
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 1.0
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 1.0
rrl 1474200 n.545delT non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474271 n.614A>G non_coding_transcript_exon_variant 1.0
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 1.0
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 1.0
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 1.0
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 1.0
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 1.0
rrl 1475767 n.2110_2111insT non_coding_transcript_exon_variant 1.0
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 1.0
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.67
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.67
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.67
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.67
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.67
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.67
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.5
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.67
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.75
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.75
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.75
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.75
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.67
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.67
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.67
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.67
rrl 1475995 n.2338G>C non_coding_transcript_exon_variant 0.67
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.92
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.94
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 1.0
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.9
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.93
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.6
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.75
rpsA 1833661 c.120A>G synonymous_variant 0.29
rpsA 1833667 c.126C>T synonymous_variant 0.29
rpsA 1833668 p.Ile43Val missense_variant 0.29
rpsA 1833676 c.135A>G synonymous_variant 0.38
rpsA 1833679 c.138G>C synonymous_variant 0.29
rpsA 1833684 p.Arg48His missense_variant 0.29
rpsA 1833694 c.153G>C synonymous_variant 0.43
rpsA 1833700 c.159C>T synonymous_variant 0.29
rpsA 1833721 c.180A>G synonymous_variant 0.2
rpsA 1834195 c.654G>C synonymous_variant 0.27
rpsA 1834234 c.693G>C synonymous_variant 0.2
rpsA 1834240 c.699T>C synonymous_variant 0.4
rpsA 1834249 c.708T>C synonymous_variant 0.44
rpsA 1834261 c.720A>G synonymous_variant 0.5
rpsA 1834264 c.723G>C synonymous_variant 0.5
rpsA 1834294 c.753G>C synonymous_variant 0.33
rpsA 1834298 p.Gln253Glu missense_variant 0.33
rpsA 1834306 c.765T>C synonymous_variant 0.4
rpsA 1834307 p.Asp256Gln missense_variant 0.4
rpsA 1834312 c.771G>A synonymous_variant 0.5
rpsA 1834327 c.786G>T synonymous_variant 0.6
rpsA 1834345 c.804C>T synonymous_variant 1.0
rpsA 1834348 c.807T>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155476 c.636T>C synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641828 c.294A>G synonymous_variant 0.11
ddn 3987191 p.Asp116Glu missense_variant 0.11
clpC1 4038743 c.1962G>A synonymous_variant 0.5
clpC1 4040009 c.696C>G synonymous_variant 0.18
clpC1 4040015 c.690G>C synonymous_variant 0.18
clpC1 4040018 c.687G>C synonymous_variant 0.18
clpC1 4040021 c.684A>C synonymous_variant 0.18
clpC1 4040024 c.681A>G synonymous_variant 0.2
clpC1 4040057 c.648C>T synonymous_variant 0.2
clpC1 4040066 c.639G>C synonymous_variant 0.2
embC 4241517 p.Leu552Ser missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248237 p.Met575Lys missense_variant 0.12
ethA 4326093 p.Tyr461Asp missense_variant 0.86
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407892 p.Met104Lys missense_variant 1.0