TB-Profiler result

Run: ERR4821712
Summary

Run ID: ERR4821712

Sample name:

Date: 01-04-2023 17:24:33

Number of reads: 400549

Percentage reads mapped: 74.23

Strain:

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
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA RD239 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 0.7 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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
gyrB 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6971 p.Pro578Ser missense_variant 0.25
gyrA 7268 c.-34C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576565 c.1218G>A synonymous_variant 0.22
ccsA 620368 p.Ala160Ser missense_variant 0.25
rpoB 760094 c.288G>T synonymous_variant 0.15
rpoB 761051 c.1245G>C synonymous_variant 0.25
rpoB 761054 c.1248G>C synonymous_variant 0.25
rpoB 761057 c.1251G>C synonymous_variant 0.25
rpoB 761060 c.1254C>G synonymous_variant 0.25
rpoB 761084 c.1278C>A synonymous_variant 0.25
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.27
rpoB 761150 c.1344A>T synonymous_variant 0.29
rpoB 761159 c.1353G>C synonymous_variant 0.29
rpoB 762625 c.2820_2821delCG frameshift_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763798 c.431_433delGCC disruptive_inframe_deletion 0.4
rpoC 764458 c.1089G>C synonymous_variant 0.25
rpoC 764461 c.1092A>G synonymous_variant 0.25
rpoC 764485 c.1116G>C synonymous_variant 0.43
rpoC 764491 c.1122G>T synonymous_variant 0.43
rpoC 764497 c.1128A>G synonymous_variant 0.5
rpoC 764503 c.1134G>T synonymous_variant 0.67
rpoC 764509 c.1140G>C synonymous_variant 0.67
rpoC 764512 c.1143G>C synonymous_variant 0.67
rpoC 764521 c.1152T>C synonymous_variant 0.8
rpoC 764524 c.1155C>T synonymous_variant 0.4
rpoC 764530 c.1161C>T synonymous_variant 0.5
rpoC 764536 c.1167G>C synonymous_variant 0.5
rpoC 764543 p.Thr392Ala missense_variant 0.57
rpoC 764548 c.1179G>C synonymous_variant 0.5
rpoC 764566 c.1197C>G synonymous_variant 0.43
rpoC 764632 c.1263T>C synonymous_variant 0.22
rpoC 764647 c.1278C>T synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777321 p.Val387Ala missense_variant 0.14
mmpL5 779269 c.-789G>T upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303828 p.His300Tyr missense_variant 0.29
Rv1258c 1406104 c.1237C>A synonymous_variant 0.14
embR 1416220 p.Phe376Leu missense_variant 0.14
embR 1416461 p.Ala296Ile missense_variant 0.29
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.75
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.73
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.73
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.64
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.94
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.59
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.63
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.35
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.31
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.91
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.44
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.29
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 0.67
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.7
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.75
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.79
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.79
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.76
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.81
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.78
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.96
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.77
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.77
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.14
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.65
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.67
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.62
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.23
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.69
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.69
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.7
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.2
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.71
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.27
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 0.86
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.33
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.4
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.8
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 1.0
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.33
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.67
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.33
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 0.92
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.83
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.17
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.2
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.89
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.67
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.7
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.67
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.67
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.67
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.67
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.3
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.3
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.8
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.78
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.88
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.86
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.86
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.86
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.86
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.62
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.62
rrs 1473122 n.1281delA non_coding_transcript_exon_variant 0.27
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.31
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.82
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.85
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.67
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.67
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.81
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.75
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.67
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.8
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.8
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.4
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.5
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.5
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.5
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 1474551 n.894G>C non_coding_transcript_exon_variant 1.0
rrl 1474555 n.898T>G non_coding_transcript_exon_variant 1.0
rrl 1474558 n.901G>C non_coding_transcript_exon_variant 1.0
rrl 1474581 n.924C>T non_coding_transcript_exon_variant 1.0
rrl 1474601 n.944C>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 1474830 n.1173A>G non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 1.0
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 1.0
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 1.0
rrl 1476164 n.2507A>T non_coding_transcript_exon_variant 0.67
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.5
rrl 1476194 n.2537A>T non_coding_transcript_exon_variant 0.67
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.67
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.67
rrl 1476207 n.2550T>C non_coding_transcript_exon_variant 0.67
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.67
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.67
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.67
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.29
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.93
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.9
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.87
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.73
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.8
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.78
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.73
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.83
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 1.0
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 1.0
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 1.0
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 1.0
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 1.0
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 1.0
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 1.0
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 1.0
rpsA 1834249 c.708T>C synonymous_variant 0.25
rpsA 1834261 c.720A>G synonymous_variant 0.21
rpsA 1834264 c.723G>C synonymous_variant 0.2
rpsA 1834294 c.753G>C synonymous_variant 0.14
rpsA 1834303 c.762T>C synonymous_variant 0.15
rpsA 1834306 c.765T>C synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 1.0
katG 2153937 c.2175C>T synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156160 c.-49T>C upstream_gene_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167928 c.2685G>A synonymous_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169805 p.Ala270Thr missense_variant 0.22
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714901 c.432A>G synonymous_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726240 c.48C>A synonymous_variant 0.18
pepQ 2860490 c.-72G>A upstream_gene_variant 0.13
thyX 3068063 c.-119_-118insG upstream_gene_variant 0.29
ald 3086672 c.-148C>T upstream_gene_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087601 p.Gly261Val missense_variant 1.0
ald 3087675 p.Pro286Ala missense_variant 0.2
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449601 p.Gln366His missense_variant 0.12
Rv3083 3449781 c.1278G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474602 p.Arg199Leu missense_variant 0.25
fprA 3474793 p.Gly263Arg missense_variant 1.0
fprA 3475090 p.Arg362Ser missense_variant 0.15
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3613249 c.-133A>T upstream_gene_variant 0.25
rpoA 3878464 p.Thr15Ile missense_variant 0.25
clpC1 4039645 p.His354Asp missense_variant 0.29
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040523 p.Ser61Ile missense_variant 0.25
clpC1 4040719 c.-15A>G upstream_gene_variant 1.0
panD 4044455 c.-174G>T upstream_gene_variant 0.13
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244926 p.Phe565Tyr missense_variant 0.25
embA 4245072 p.Leu614Val missense_variant 0.17
embB 4245704 c.-810G>A upstream_gene_variant 0.25
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4269252 c.-416C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407566 c.637C>A synonymous_variant 0.2
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407848 p.Ala119Thr missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407926 p.Pro93Ser missense_variant 1.0