TB-Profiler result

Run: ERR4769502
Summary

Run ID: ERR4769502

Sample name:

Date: 01-04-2023 06:42:55

Number of reads: 50663

Percentage reads mapped: 2.51

Strain: lineage4.9;La1.3

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
La1.3 M.bovis None None 0.15
lineage4 Euro-American LAM;T;S;X;H None 0.99
lineage4.9 Euro-American (H37Rv-like) T1 None 0.89
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 761127 p.Ser441Ala missense_variant 0.67 rifampicin
rpoB 761131 p.Gly442Glu missense_variant 0.67 rifampicin
rpoB 761196 p.Leu464Met missense_variant 0.75 rifampicin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.62 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.5 kanamycin, capreomycin, aminoglycosides, amikacin
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide
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 6406 c.-896C>T upstream_gene_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
rpoB 761133 p.Leu443Met missense_variant 0.67
rpoB 761138 c.1332C>G synonymous_variant 0.67
rpoB 761150 c.1344A>T synonymous_variant 0.75
rpoB 761159 c.1353G>C synonymous_variant 0.75
rpoB 761165 c.1359G>C synonymous_variant 0.75
rpoB 761177 c.1371G>C synonymous_variant 0.75
rpoB 761180 c.1374A>C synonymous_variant 0.75
rpoB 761183 c.1377T>C synonymous_variant 0.75
rpoB 761186 p.Glu460Asp missense_variant 0.75
rpoB 761189 c.1383T>C synonymous_variant 0.75
rpoB 761195 c.1389G>C synonymous_variant 0.75
rpoB 761207 c.1401C>T synonymous_variant 0.75
rpoB 761213 c.1407G>C synonymous_variant 0.75
rpoB 761220 c.1414_1416delTCGinsAGC synonymous_variant 1.0
rpoB 761231 c.1425C>G synonymous_variant 1.0
rpoB 761249 c.1443A>G synonymous_variant 0.75
rpoB 761255 c.1449T>C synonymous_variant 0.5
rpoC 763546 c.177A>G synonymous_variant 0.75
rpoC 763570 c.201G>C synonymous_variant 0.67
rpoC 763589 p.Ile74Val missense_variant 0.67
rpoC 763594 c.225C>T synonymous_variant 0.67
rpoC 763600 c.231C>G synonymous_variant 0.67
rpoC 763609 c.240C>G synonymous_variant 0.67
rpoC 763615 c.246G>C synonymous_variant 0.67
rpoC 763621 c.252C>T synonymous_variant 0.67
rpoC 763622 p.Ala85Ser missense_variant 0.67
rpoC 763627 p.Lys86Asn missense_variant 0.67
rpoC 763633 c.264T>C synonymous_variant 0.67
rpoC 763642 c.273G>C synonymous_variant 0.67
rpoC 763656 c.287_288insACT disruptive_inframe_insertion 0.75
rpoC 763659 p.Leu97Arg missense_variant 0.75
rpoC 763663 c.295_297delGCG conservative_inframe_deletion 0.75
rpoC 764632 c.1263T>C synonymous_variant 1.0
rpoC 764650 c.1281G>T synonymous_variant 1.0
rpoC 764653 c.1284G>T synonymous_variant 1.0
rpoC 764662 c.1293G>C synonymous_variant 1.0
rpoC 764668 c.1299C>T synonymous_variant 1.0
rpoC 764677 c.1308C>G synonymous_variant 1.0
rpoC 764681 p.Leu438Met missense_variant 1.0
rpoC 764695 c.1326T>C synonymous_variant 0.67
rpoC 764706 p.Leu446Gln missense_variant 0.67
rpoC 764731 c.1362G>C synonymous_variant 0.67
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.67
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.6
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.6
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.6
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 0.67
rrs 1472288 n.443A>C non_coding_transcript_exon_variant 0.67
rrs 1472289 n.444T>A non_coding_transcript_exon_variant 0.67
rrs 1472290 n.445C>T non_coding_transcript_exon_variant 0.67
rrs 1472297 n.453_461delGTCCGGGTT non_coding_transcript_exon_variant 0.67
rrs 1472309 n.464C>T non_coding_transcript_exon_variant 0.67
rrs 1472311 n.466C>T non_coding_transcript_exon_variant 0.67
rrs 1472312 n.468_470delGAT non_coding_transcript_exon_variant 0.67
rrs 1472325 n.480G>T non_coding_transcript_exon_variant 0.67
rrs 1472326 n.481T>G non_coding_transcript_exon_variant 0.67
rrs 1472329 n.484A>G non_coding_transcript_exon_variant 0.67
rrs 1472368 n.523A>G non_coding_transcript_exon_variant 0.67
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 1.0
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 1.0
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.67
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.67
rrs 1472957 n.1112C>A non_coding_transcript_exon_variant 1.0
rrs 1472969 n.1125delC non_coding_transcript_exon_variant 0.67
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 1.0
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.67
rrs 1472975 n.1130T>G non_coding_transcript_exon_variant 0.67
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.67
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.67
rrs 1472989 n.1144G>T non_coding_transcript_exon_variant 1.0
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.67
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.67
rrs 1473029 n.1184C>G non_coding_transcript_exon_variant 0.83
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.75
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.33
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.33
rrs 1473091 n.1246G>A non_coding_transcript_exon_variant 0.67
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.67
rrs 1473099 n.1254T>G non_coding_transcript_exon_variant 1.0
rrs 1473100 n.1255G>C non_coding_transcript_exon_variant 1.0
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.67
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 1.0
rrs 1473109 n.1264T>G non_coding_transcript_exon_variant 0.67
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.33
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 1.0
rrs 1473120 n.1275C>T non_coding_transcript_exon_variant 0.67
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 1.0
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.67
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 1.0
rrs 1473129 n.1284C>T non_coding_transcript_exon_variant 0.29
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.75
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.67
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.67
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.71
rrs 1473284 n.1439A>G non_coding_transcript_exon_variant 0.5
rrs 1473285 n.1440A>T non_coding_transcript_exon_variant 0.5
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.6
rrs 1473293 n.1449delA non_coding_transcript_exon_variant 0.5
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.67
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.5
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.5
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.5
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.5
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.43
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.5
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.5
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.5
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.57
rrl 1474798 n.1141C>G non_coding_transcript_exon_variant 0.67
rrl 1474800 n.1143T>G non_coding_transcript_exon_variant 0.67
rrl 1474801 n.1144G>T non_coding_transcript_exon_variant 0.67
rrl 1474802 n.1145T>G non_coding_transcript_exon_variant 0.67
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.8
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.8
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.8
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.8
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.8
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.8
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.8
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.5
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.5
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.5
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.5
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.5
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.57
rrl 1475880 n.2223C>G non_coding_transcript_exon_variant 0.5
rrl 1475881 n.2224T>G non_coding_transcript_exon_variant 0.5
rrl 1475882 n.2225C>G non_coding_transcript_exon_variant 0.5
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.5
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.33
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.5
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.33
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.5
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.5
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.5
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.6
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 1.0
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.75
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.75
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.75
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.5
rrl 1476032 n.2375C>G non_coding_transcript_exon_variant 0.5
rrl 1476033 n.2376T>G non_coding_transcript_exon_variant 0.5
rrl 1476034 n.2377C>T non_coding_transcript_exon_variant 0.5
rrl 1476045 n.2388G>A non_coding_transcript_exon_variant 0.5
rrl 1476046 n.2389G>T non_coding_transcript_exon_variant 0.5
rrl 1476047 n.2390G>C non_coding_transcript_exon_variant 0.5
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.5
rrl 1476080 n.2423T>A non_coding_transcript_exon_variant 0.67
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.67
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.67
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.6
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.67
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 1.0
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 1.0
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 1.0
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 1.0
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 1.0
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 1.0
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 1.0
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 1.0
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 1.0
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 1.0
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 1.0
rrl 1476300 n.2643G>A non_coding_transcript_exon_variant 1.0
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 1.0
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.82
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.27
rrl 1476481 n.2824T>A non_coding_transcript_exon_variant 0.33
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.29
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.5
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.67
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 1.0
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 1.0
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 1.0
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.67
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.67
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.67
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.67
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.67
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.67
rrl 1476728 n.3071T>C non_coding_transcript_exon_variant 1.0
rpsA 1833997 c.456G>C synonymous_variant 0.67
rpsA 1834000 c.459G>C synonymous_variant 0.67
rpsA 1834012 c.471G>C synonymous_variant 0.67
rpsA 1834015 c.474G>C synonymous_variant 0.67
rpsA 1834034 p.Ile165Val missense_variant 0.67
rpsA 1834039 c.498C>T synonymous_variant 0.67
rpsA 1834040 p.Lys167Gln missense_variant 0.67
rpsA 1834046 p.Ile169Leu missense_variant 0.67
rpsA 1834054 c.513C>G synonymous_variant 0.67
rpsA 1834066 c.525G>A synonymous_variant 0.67
rpsA 1834069 c.528G>C synonymous_variant 0.67
rpsA 1834090 c.549G>C synonymous_variant 0.67
rpsA 1834093 c.552G>C synonymous_variant 0.67
rpsA 1834099 c.558C>G synonymous_variant 0.67
rpsA 1834105 c.564C>T synonymous_variant 0.67
rpsA 1834114 c.573G>C synonymous_variant 0.67
katG 2154724 p.Arg463Leu missense_variant 1.0
Rv2752c 3065003 p.His397Tyr missense_variant 0.67
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3841434 c.-14C>T upstream_gene_variant 0.4
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0