TB-Profiler result

Run: ERR4818574
Summary

Run ID: ERR4818574

Sample name:

Date: 01-04-2023 15:38:08

Number of reads: 745553

Percentage reads mapped: 89.59

Strain: lineage6

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
lineage6 West-Africa 2 AFRI_1 RD702 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.25 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.47 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.3 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.18 kanamycin, capreomycin, aminoglycosides, amikacin
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 6446 p.Ala403Ser missense_variant 1.0
gyrA 6934 c.-368A>G upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8493 p.Leu398Phe missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.24
fgd1 491668 p.Lys296Glu missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575231 c.-117G>A upstream_gene_variant 0.12
mshA 576157 c.810C>T synonymous_variant 0.17
mshA 576751 p.Lys468Asn missense_variant 0.5
rpoB 760855 p.Thr350Ile missense_variant 1.0
rpoB 760969 p.Ser388Leu missense_variant 1.0
rpoB 761723 p.Glu639Asp missense_variant 1.0
rpoB 762879 p.Met1025Leu missense_variant 0.11
rpoC 762902 c.-468C>T upstream_gene_variant 0.16
rpoC 762911 c.-459C>T upstream_gene_variant 0.15
rpoC 762917 c.-453C>T upstream_gene_variant 0.19
rpoC 762989 c.-381G>C upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766231 c.2862T>C synonymous_variant 1.0
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
Rv1258c 1406685 p.Val219Ala missense_variant 1.0
embR 1416633 p.Leu239Val missense_variant 1.0
atpE 1461251 c.207G>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.19
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.19
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.21
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.24
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.53
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.23
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.18
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.41
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.37
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.12
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.13
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.5
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.5
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.4
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.29
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.25
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.5
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.57
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.6
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.6
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.13
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.47
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.13
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.6
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.43
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.64
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.14
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.5
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.15
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.15
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.54
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.62
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.58
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.35
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.41
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.35
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.29
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.38
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.41
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.41
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.12
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.41
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.41
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.41
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.42
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.42
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.29
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.25
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.18
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.17
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.18
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.67
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.68
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.69
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.81
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.79
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.84
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.78
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.74
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.86
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.89
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.85
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.91
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.86
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.85
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.73
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.81
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.63
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.78
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.78
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.78
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.63
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.73
rrs 1473122 n.1278A>T non_coding_transcript_exon_variant 0.15
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.16
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.74
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.68
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.12
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.15
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.12
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.14
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.15
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.15
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.15
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.55
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.15
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.55
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.15
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.3
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.5
rrs 1473288 n.1443C>T non_coding_transcript_exon_variant 0.38
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.44
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.23
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.38
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.13
rrl 1473679 n.22T>C non_coding_transcript_exon_variant 0.18
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.6
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.5
rrl 1474393 n.736A>G non_coding_transcript_exon_variant 0.5
rrl 1474402 n.745T>C non_coding_transcript_exon_variant 0.5
rrl 1474413 n.757_776delCCCACACGCGCATACGCGCG non_coding_transcript_exon_variant 0.5
rrl 1474437 n.781_782delAA non_coding_transcript_exon_variant 0.4
rrl 1474448 n.791T>C non_coding_transcript_exon_variant 0.33
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.5
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.71
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.71
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.78
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.78
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.78
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.78
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.62
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.56
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.56
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.33
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.3
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.5
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.5
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.44
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.44
rrl 1475757 n.2101_2104delACCC non_coding_transcript_exon_variant 0.25
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.31
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.31
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 1.0
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.25
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.43
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.33
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.29
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.22
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.22
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.2
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.2
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.33
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.23
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.15
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.15
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.15
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.25
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.63
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.71
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.81
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.78
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.79
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.62
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.44
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.15
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.25
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.25
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.25
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.18
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.2
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.2
inhA 1674434 p.Val78Ala missense_variant 1.0
rpsA 1834030 c.489C>T synonymous_variant 0.12
rpsA 1834039 c.498C>T synonymous_variant 0.13
rpsA 1834040 p.Lys167Gln missense_variant 0.12
rpsA 1834043 p.Glu168Gln missense_variant 0.13
rpsA 1834051 c.510G>A synonymous_variant 0.13
rpsA 1834054 c.513C>T synonymous_variant 0.14
rpsA 1834090 c.549G>T synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.13
PPE35 2169581 c.1032C>G synonymous_variant 0.15
PPE35 2169587 c.1026G>A synonymous_variant 0.16
PPE35 2170190 p.Glu141Asp missense_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289858 c.-617G>T upstream_gene_variant 0.17
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.2
ahpC 2726449 p.Ser86Trp missense_variant 0.11
pepQ 2859920 p.Arg167* stop_gained 0.13
thyA 3074262 c.210T>C synonymous_variant 0.22
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
Rv3083 3449396 p.Cys298Tyr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612143 p.Arg325His missense_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.17
panD 4044432 c.-151T>G upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241713 c.1851G>A synonymous_variant 0.2
embC 4241715 p.Asn618Thr missense_variant 0.22
embC 4241720 p.Thr620Ser missense_variant 0.22
embC 4241723 c.1862delT frameshift_variant 0.25
embC 4241727 c.1867_1868delGC frameshift_variant 0.25
embC 4241843 p.Leu661Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244379 p.Pro383Ser missense_variant 1.0
embA 4245351 p.Lys707Glu missense_variant 0.14
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247427 p.Gly305Ala missense_variant 0.1
embB 4247437 c.924A>G synonymous_variant 0.11
embB 4247440 c.927C>G synonymous_variant 0.11
embB 4247441 p.Ala310Ser missense_variant 0.12
embB 4247446 p.Asp311Glu missense_variant 0.12
embB 4247449 c.936C>T synonymous_variant 0.12
embB 4247452 c.939C>G synonymous_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269522 c.-686C>T upstream_gene_variant 0.92
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
aftB 4269693 c.-857C>T upstream_gene_variant 1.0
ethA 4326465 p.Ile337Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408034 p.Glu57Lys missense_variant 1.0