TB-Profiler result

Run: ERR2514389
Summary

Run ID: ERR2514389

Sample name:

Date: 31-03-2023 20:18:26

Number of reads: 394432

Percentage reads mapped: 94.01

Strain: lineage3

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
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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.5 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.67 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 5192 c.-48C>T upstream_gene_variant 0.11
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 759615 c.-192A>C upstream_gene_variant 0.22
rpoB 759711 c.-95_-88delGCCGAAAC upstream_gene_variant 0.33
rpoB 759723 c.-84C>T upstream_gene_variant 0.33
rpoB 759726 c.-81A>T upstream_gene_variant 0.33
rpoB 759727 c.-80A>T upstream_gene_variant 0.33
rpoB 759730 c.-77A>G upstream_gene_variant 0.33
rpoB 759733 c.-74_-73insGTTTCGGC upstream_gene_variant 0.4
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762521 c.-849C>T upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766582 c.3213C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776872 p.Glu537Lys missense_variant 0.15
mmpL5 777482 c.999G>A synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304901 c.1971C>G synonymous_variant 0.29
fbiC 1305463 p.Arg845Cys missense_variant 0.14
Rv1258c 1406147 c.1194C>G synonymous_variant 0.25
embR 1416772 c.576C>A synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471701 n.-145A>G upstream_gene_variant 0.12
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.4
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.5
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.5
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.22
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.22
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.22
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.22
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.22
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.22
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.22
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.22
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.44
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.22
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.22
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.22
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.29
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.67
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.5
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.67
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.67
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.67
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.67
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.67
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.5
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.5
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.5
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.58
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.54
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.54
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.69
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.15
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.15
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.64
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 0.6
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.6
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.6
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.75
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.75
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.75
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.6
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.6
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.4
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.6
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.6
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.5
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.2
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.15
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.15
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.18
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.56
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.62
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.5
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.25
rrs 1473291 n.1446G>C non_coding_transcript_exon_variant 0.33
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.29
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.22
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.43
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.38
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 1475775 n.2118G>T non_coding_transcript_exon_variant 0.67
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.5
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.5
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.5
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.5
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.5
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.71
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.71
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.71
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.6
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.57
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.67
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.33
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.33
rrl 1476600 n.2943A>C non_coding_transcript_exon_variant 0.33
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.33
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.33
rrl 1476616 n.2959A>G non_coding_transcript_exon_variant 0.33
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.33
rrl 1476628 n.2971T>G non_coding_transcript_exon_variant 0.29
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.29
rrl 1476630 n.2973A>C non_coding_transcript_exon_variant 0.29
rrl 1476633 n.2976A>G non_coding_transcript_exon_variant 0.29
rpsA 1834157 c.616T>C synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102841 p.Ile68Phe missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154914 p.His400Tyr missense_variant 0.2
katG 2155672 p.Leu147Pro missense_variant 0.25
katG 2155919 c.190_192delTAT conservative_inframe_deletion 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.13
PPE35 2167967 c.2646A>C synonymous_variant 0.12
PPE35 2170415 c.198A>G synonymous_variant 0.2
PPE35 2170424 c.189G>C synonymous_variant 0.2
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
kasA 2518809 p.Lys232Arg missense_variant 0.12
kasA 2518816 c.702C>A synonymous_variant 0.11
kasA 2518822 c.708C>G synonymous_variant 0.11
kasA 2518825 c.711T>C synonymous_variant 0.11
kasA 2518855 c.741C>G synonymous_variant 0.11
kasA 2518864 c.750G>C synonymous_variant 0.11
kasA 2518879 c.765A>G synonymous_variant 0.12
kasA 2518885 c.771T>C synonymous_variant 0.12
kasA 2518888 c.774C>T synonymous_variant 0.12
kasA 2518898 c.784T>C synonymous_variant 0.14
kasA 2518906 c.792A>G synonymous_variant 0.13
kasA 2518910 p.Leu266Met missense_variant 0.13
kasA 2519153 p.Ile347Val missense_variant 0.67
eis 2714569 p.Ala255Gly missense_variant 0.22
eis 2715019 p.His105Arg missense_variant 0.15
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.23
thyA 3074645 c.-174T>G upstream_gene_variant 0.33
thyA 3074648 c.-177T>G upstream_gene_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448514 p.His4Leu missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 1.0
clpC1 4039654 p.Thr351Ser missense_variant 0.25
clpC1 4039916 c.789T>G synonymous_variant 0.25
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245610 p.Val793Ala missense_variant 0.22
embB 4248041 p.Ala510Thr missense_variant 0.11
ethA 4326496 c.978G>A synonymous_variant 0.1
whiB6 4338485 p.Asn13Tyr missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0