TB-Profiler result

Run: ERR2509885
Summary

Run ID: ERR2509885

Sample name:

Date: 31-03-2023 18:32:50

Number of reads: 628273

Percentage reads mapped: 83.5

Strain: lineage3

Drug-resistance: RR-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 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
rpoB 761098 p.Ser431Thr missense_variant 0.11 rifampicin
rpoB 761127 p.Ser441Ala missense_variant 0.14 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.56 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
gyrB 6981 p.Ala581Val missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7445 c.144C>T synonymous_variant 0.2
gyrA 7446 p.Lys49Glu missense_variant 0.2
gyrA 7455 p.His52Asn missense_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8360 c.1059G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9623 c.2322G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761051 c.1245G>C synonymous_variant 0.12
rpoB 761054 c.1248G>C synonymous_variant 0.12
rpoB 761057 c.1251G>C synonymous_variant 0.12
rpoB 761060 c.1254C>G synonymous_variant 0.12
rpoB 761084 c.1278C>A synonymous_variant 0.12
rpoB 761088 p.Ser428Cys missense_variant 0.11
rpoB 761096 c.1290G>C synonymous_variant 0.11
rpoB 761102 c.1296A>G synonymous_variant 0.11
rpoB 761133 c.1327T>C synonymous_variant 0.14
rpoB 761147 c.1341C>T synonymous_variant 0.13
rpoB 761165 c.1359G>C synonymous_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764566 c.1197C>G synonymous_variant 0.11
rpoC 764575 c.1206T>C synonymous_variant 0.14
rpoC 764581 c.1212T>C synonymous_variant 0.19
rpoC 764582 p.Leu405Met missense_variant 0.17
rpoC 764611 c.1242G>T synonymous_variant 0.17
rpoC 764632 c.1263T>C synonymous_variant 0.12
rpoC 764650 c.1281G>C synonymous_variant 0.12
rpoC 764665 c.1296C>G synonymous_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777052 p.Gly477Arg missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.21
fbiC 1305073 p.Ser715Cys missense_variant 0.11
embR 1416426 c.919_921delGCG conservative_inframe_deletion 0.16
embR 1416436 c.911_912insGTGGGT disruptive_inframe_insertion 0.16
embR 1416440 c.902_907delACCCAC disruptive_inframe_deletion 0.17
atpE 1461082 p.Gly13Ala missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.12
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.11
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.11
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.13
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 0.15
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.34
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.38
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.37
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.51
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.5
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.48
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.48
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.11
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.46
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.55
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.49
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.62
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.6
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.6
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.28
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.57
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.47
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.12
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.44
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.45
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.3
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.5
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.44
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.57
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.57
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.54
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.53
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.4
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.34
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.33
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.16
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.11
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.11
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.13
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.17
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.18
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.27
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.26
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.32
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.31
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.26
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.39
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.51
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.43
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.49
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.43
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.41
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.39
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.42
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.4
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.42
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.41
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.41
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.38
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.42
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.38
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.38
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.26
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.26
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.24
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.26
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.19
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.13
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.11
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.1
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.17
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.11
rrl 1475290 n.1633A>G non_coding_transcript_exon_variant 0.17
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.17
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.15
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.2
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.2
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.16
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.21
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.2
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.17
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.25
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.23
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.23
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.18
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.25
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.23
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.23
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.15
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.23
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.21
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.43
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.19
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.18
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.15
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.14
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.13
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.12
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.16
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.36
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.38
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.35
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.32
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.38
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.27
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>A synonymous_variant 0.11
Rv1979c 2222273 p.Ala298Ser missense_variant 1.0
Rv1979c 2222826 c.338dupT frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.29
folC 2746416 p.Glu395Lys missense_variant 0.1
folC 2747618 c.-20A>G upstream_gene_variant 0.12
pepQ 2859621 c.797delC frameshift_variant 0.22
ribD 2986752 c.-87C>G upstream_gene_variant 1.0
Rv2752c 3066219 c.-28T>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087917 c.1098C>G synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474115 p.Asp37Asn missense_variant 0.13
whiB7 3568665 c.14_15insT frameshift_variant 1.0
Rv3236c 3612568 c.549G>C synonymous_variant 0.29
fbiA 3640880 c.340dupG frameshift_variant 0.12
fbiA 3640888 c.349delC frameshift_variant 0.13
alr 3840211 p.Glu404* stop_gained 1.0
alr 3840688 c.732delC frameshift_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247358 p.Val282Ala missense_variant 0.1
embB 4249796 p.Arg1095* stop_gained 0.2
aftB 4268060 c.777C>T synonymous_variant 0.14
ethR 4327813 p.Thr89Pro missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0