TB-Profiler result

Run: ERR017781
Summary

Run ID: ERR017781

Sample name:

Date: 31-03-2023 07:55:56

Number of reads: 1584847

Percentage reads mapped: 37.58

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 0.99
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 1473247 n.1402C>A non_coding_transcript_exon_variant 0.76 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.59 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
gyrA 7362 p.Glu21Gln missense_variant 0.97
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
ccsA 620748 c.858T>G synonymous_variant 0.44
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761042 c.1236C>T synonymous_variant 0.2
rpoB 761051 c.1245G>C synonymous_variant 0.25
rpoB 761054 c.1248G>A synonymous_variant 0.25
rpoB 761058 p.Val418Thr missense_variant 0.2
rpoB 761063 c.1257C>A synonymous_variant 0.17
rpoB 761084 c.1278C>A synonymous_variant 0.17
rpoB 761207 c.1401C>T synonymous_variant 0.29
rpoB 761213 c.1407G>T synonymous_variant 0.35
rpoB 761231 c.1425C>T synonymous_variant 0.38
rpoB 761234 c.1428G>T synonymous_variant 0.35
rpoB 761246 c.1440C>T synonymous_variant 0.4
rpoB 762053 c.2247T>C synonymous_variant 0.11
rpoB 762057 p.Ile751Val missense_variant 0.12
rpoB 762062 c.2256T>C synonymous_variant 0.12
rpoB 762068 c.2262C>T synonymous_variant 0.13
rpoB 762071 c.2265C>T synonymous_variant 0.13
rpoB 762218 c.2412T>C synonymous_variant 0.15
rpoB 762233 c.2427G>C synonymous_variant 0.23
rpoB 762236 c.2430G>T synonymous_variant 0.27
rpoB 762245 c.2439G>T synonymous_variant 0.27
rpoB 762254 c.2448T>C synonymous_variant 0.31
rpoB 762257 c.2451C>G synonymous_variant 0.29
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762489 p.Val895Phe missense_variant 0.33
rpoB 762878 p.Ile1024Met missense_variant 0.27
rpoB 762879 p.Met1025Leu missense_variant 0.31
rpoC 762899 c.-471G>C upstream_gene_variant 0.46
rpoC 762920 c.-450C>T upstream_gene_variant 0.64
rpoC 762929 c.-441G>C upstream_gene_variant 0.6
rpoC 762935 c.-435C>T upstream_gene_variant 0.55
rpoC 762959 c.-411G>T upstream_gene_variant 0.44
rpoC 762971 c.-399G>C upstream_gene_variant 0.31
rpoC 762983 c.-387C>T upstream_gene_variant 0.23
rpoC 762989 c.-381G>A upstream_gene_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 0.93
rpoC 763085 c.-285C>T upstream_gene_variant 0.12
rpoC 763094 c.-276G>C upstream_gene_variant 0.11
rpoC 763097 c.-273C>T upstream_gene_variant 0.11
rpoC 763115 c.-255T>C upstream_gene_variant 0.11
rpoC 763124 c.-246C>T upstream_gene_variant 0.14
rpoC 763127 c.-243G>T upstream_gene_variant 0.19
rpoC 763528 c.159G>A synonymous_variant 0.48
rpoC 763534 c.165T>C synonymous_variant 0.52
rpoC 763537 c.168C>G synonymous_variant 0.5
rpoC 763546 c.177A>G synonymous_variant 0.52
rpoC 763570 c.201G>C synonymous_variant 0.47
rpoC 763573 c.204G>C synonymous_variant 0.43
rpoC 763594 c.225C>T synonymous_variant 0.54
rpoC 763622 p.Ala85Ser missense_variant 0.5
rpoC 763627 p.Lys86Asn missense_variant 0.48
rpoC 763642 c.273G>T synonymous_variant 0.25
rpoC 763648 c.279C>A synonymous_variant 0.12
rpoC 764875 c.1506C>G synonymous_variant 0.12
rpoC 764878 c.1509C>G synonymous_variant 0.11
rpoC 764887 c.1518G>C synonymous_variant 0.15
rpoC 764888 c.1519T>C synonymous_variant 0.14
rpoC 764896 c.1527C>T synonymous_variant 0.14
rpoC 767002 c.3633G>C synonymous_variant 0.18
rpoC 767012 c.3643C>T synonymous_variant 0.17
rpoC 767023 p.Asp1218Glu missense_variant 0.21
rpoC 767030 c.3661C>T synonymous_variant 0.17
rpoC 767314 p.Tyr1315* stop_gained 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775937 c.2544G>A synonymous_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781655 c.96T>C synonymous_variant 0.14
rpsL 781658 c.99A>G synonymous_variant 0.17
rpsL 781667 c.108C>T synonymous_variant 0.21
rpsL 781679 c.120C>G synonymous_variant 0.27
rpsL 781682 c.123T>G synonymous_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471923 n.78T>C non_coding_transcript_exon_variant 0.18
rrs 1471981 n.136C>G non_coding_transcript_exon_variant 0.1
rrs 1472085 n.240C>T non_coding_transcript_exon_variant 0.33
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.55
rrs 1472107 n.262A>G non_coding_transcript_exon_variant 0.55
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.55
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.59
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.68
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.66
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.69
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.85
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.85
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.86
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.87
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.84
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 0.63
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 0.26
rrs 1472288 n.443A>T non_coding_transcript_exon_variant 0.12
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.12
rrs 1472290 n.445C>T non_coding_transcript_exon_variant 0.11
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.66
rrs 1472368 n.523A>G non_coding_transcript_exon_variant 0.82
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.76
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.72
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.62
rrs 1472427 n.582T>G non_coding_transcript_exon_variant 0.15
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.2
rrs 1472507 n.662C>A non_coding_transcript_exon_variant 0.55
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.66
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.71
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.69
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.55
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.55
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.53
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.53
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.82
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.8
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.26
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.16
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.18
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.21
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.19
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.4
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.54
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.54
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.84
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.81
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 0.7
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.79
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.79
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.86
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.69
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.7
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.82
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.85
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.76
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.58
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 0.25
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.7
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.8
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.8
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.83
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.76
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.67
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.3
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.3
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.3
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.3
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.52
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.49
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.53
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.55
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.59
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 0.25
rrl 1473836 n.179A>T non_coding_transcript_exon_variant 0.29
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.37
rrl 1473862 n.205C>T non_coding_transcript_exon_variant 0.62
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.65
rrl 1473887 n.230T>G non_coding_transcript_exon_variant 0.61
rrl 1474166 n.509G>T non_coding_transcript_exon_variant 0.5
rrl 1474167 n.510T>C non_coding_transcript_exon_variant 0.5
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.56
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.6
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.72
rrl 1474202 n.545T>G non_coding_transcript_exon_variant 0.71
rrl 1474218 n.561T>G non_coding_transcript_exon_variant 0.78
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.42
rrl 1474454 n.797G>A non_coding_transcript_exon_variant 0.73
rrl 1474467 n.810A>T non_coding_transcript_exon_variant 0.64
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.59
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.67
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 0.38
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.38
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.38
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.38
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.38
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.71
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.71
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.83
rrl 1474707 n.1051_1052delCG non_coding_transcript_exon_variant 0.4
rrl 1474711 n.1055_1056insCAAG non_coding_transcript_exon_variant 0.38
rrl 1474715 n.1060_1061delAA non_coding_transcript_exon_variant 0.4
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.79
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.77
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.73
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.17
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.12
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.68
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.7
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.7
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.7
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.84
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.88
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.78
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.78
rrl 1474928 n.1271C>T non_coding_transcript_exon_variant 0.5
rrl 1475119 n.1462C>T non_coding_transcript_exon_variant 0.17
rrl 1475124 n.1467A>T non_coding_transcript_exon_variant 0.25
rrl 1475137 n.1480A>T non_coding_transcript_exon_variant 0.3
rrl 1475170 n.1513A>G non_coding_transcript_exon_variant 0.17
rrl 1475171 n.1514C>T non_coding_transcript_exon_variant 0.15
rrl 1475175 n.1518G>C non_coding_transcript_exon_variant 0.18
rrl 1475176 n.1519G>A non_coding_transcript_exon_variant 0.18
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.23
rrl 1475499 n.1842C>T non_coding_transcript_exon_variant 0.25
rrl 1475510 n.1853A>T non_coding_transcript_exon_variant 0.33
rrl 1475516 n.1859T>A non_coding_transcript_exon_variant 0.31
rrl 1475517 n.1860C>T non_coding_transcript_exon_variant 0.31
rrl 1475526 n.1869C>T non_coding_transcript_exon_variant 0.31
rrl 1475532 n.1875A>G non_coding_transcript_exon_variant 0.33
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.25
rrl 1475586 n.1929C>T non_coding_transcript_exon_variant 0.19
rrl 1475591 n.1934G>T non_coding_transcript_exon_variant 0.18
rrl 1475602 n.1945G>T non_coding_transcript_exon_variant 0.17
rrl 1475661 n.2004G>A non_coding_transcript_exon_variant 0.2
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.7
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.82
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.83
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.24
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.36
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.46
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.82
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.79
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.68
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.68
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.67
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.57
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.55
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.71
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.85
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.85
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.84
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.4
rrl 1476117 n.2460G>A non_coding_transcript_exon_variant 0.18
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.36
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.36
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.75
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.86
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.83
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.83
rrl 1476194 n.2537A>T non_coding_transcript_exon_variant 0.88
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.88
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.88
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.88
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.88
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.76
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.67
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.7
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.65
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.62
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.63
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.46
rrl 1476290 n.2633C>T non_coding_transcript_exon_variant 0.16
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.71
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.64
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.67
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.65
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.68
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.72
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.77
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.82
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.82
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.87
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.8
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.7
rpsA 1834040 p.Lys167Gln missense_variant 0.1
rpsA 1834069 c.528G>C synonymous_variant 0.48
rpsA 1834090 c.549G>T synonymous_variant 0.51
rpsA 1834099 c.558C>G synonymous_variant 0.53
rpsA 1834105 c.564C>T synonymous_variant 0.32
rpsA 1834108 c.567C>G synonymous_variant 0.21
rpsA 1834114 c.573G>C synonymous_variant 0.14
rpsA 1834240 c.699T>C synonymous_variant 0.33
rpsA 1834243 c.702G>A synonymous_variant 0.27
rpsA 1834246 c.705G>C synonymous_variant 0.27
rpsA 1834261 c.720A>G synonymous_variant 0.15
rpsA 1834264 c.723G>C synonymous_variant 0.15
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289558 c.-317C>T upstream_gene_variant 0.25
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568799 c.-120A>C upstream_gene_variant 0.33
fbiB 3642877 p.Lys448Arg missense_variant 0.92
rpoA 3878241 c.267G>A synonymous_variant 0.14
rpoA 3878253 p.Val85Leu missense_variant 0.13
rpoA 3878264 p.Ser82Gly missense_variant 0.11
rpoA 3878271 c.237T>C synonymous_variant 0.12
rpoA 3878277 c.231C>T synonymous_variant 0.12
rpoA 3878400 c.108T>C synonymous_variant 0.67
rpoA 3878406 p.Leu34Ile missense_variant 0.67
rpoA 3878415 c.93C>A synonymous_variant 0.57
rpoA 3878421 c.87A>T synonymous_variant 0.43
rpoA 3878641 c.-135delG upstream_gene_variant 1.0
clpC1 4039670 p.Val345Ile missense_variant 0.15
clpC1 4039685 c.1020C>T synonymous_variant 0.56
clpC1 4039694 c.1011G>C synonymous_variant 0.53
clpC1 4039718 c.987C>T synonymous_variant 0.39
clpC1 4039724 c.981A>G synonymous_variant 0.33
clpC1 4039733 c.972G>C synonymous_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.91
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0