TB-Profiler result

Run: ERR2512986
Summary

Run ID: ERR2512986

Sample name:

Date: 31-03-2023 19:23:14

Number of reads: 2054432

Percentage reads mapped: 76.88

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 1472733 n.888G>A non_coding_transcript_exon_variant 0.58 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
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
mshA 575160 c.-187delT upstream_gene_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761030 c.1224G>C synonymous_variant 0.14
rpoB 761037 c.1231T>C synonymous_variant 0.12
rpoB 761452 p.Val549Ala missense_variant 0.12
rpoB 762071 p.Asp755Glu missense_variant 0.1
rpoB 762080 c.2274G>C synonymous_variant 0.12
rpoB 762085 p.Ala760Glu missense_variant 0.15
rpoB 762089 c.2283G>A synonymous_variant 0.2
rpoB 762110 c.2304G>C synonymous_variant 0.19
rpoB 762114 p.Ile770Val missense_variant 0.21
rpoB 762122 p.Asp772Glu missense_variant 0.19
rpoB 762125 c.2319G>A synonymous_variant 0.21
rpoB 762126 p.Val774Ser missense_variant 0.21
rpoB 762134 c.2328C>T synonymous_variant 0.24
rpoB 762143 c.2337T>C synonymous_variant 0.27
rpoB 762149 c.2343G>C synonymous_variant 0.25
rpoB 762156 p.Val784Ile missense_variant 0.25
rpoB 762176 c.2370T>C synonymous_variant 0.23
rpoB 762177 p.Arg791Thr missense_variant 0.23
rpoB 762181 p.Asp792Ala missense_variant 0.22
rpoB 762185 c.2379G>C synonymous_variant 0.22
rpoB 762194 c.2388G>C synonymous_variant 0.21
rpoB 762200 c.2394C>T synonymous_variant 0.23
rpoB 762218 c.2412T>C synonymous_variant 0.17
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763397 p.Leu10Ile missense_variant 0.11
rpoC 764497 c.1128A>G synonymous_variant 0.16
rpoC 764503 c.1134G>T synonymous_variant 0.14
rpoC 764509 c.1140G>C synonymous_variant 0.14
rpoC 764512 c.1143G>C synonymous_variant 0.13
rpoC 764536 c.1167G>C synonymous_variant 0.12
rpoC 764543 p.Thr392Ala missense_variant 0.12
rpoC 764548 c.1179G>C synonymous_variant 0.11
rpoC 764566 c.1197C>G synonymous_variant 0.15
rpoC 764573 p.Leu402Ile missense_variant 0.15
rpoC 764578 c.1209C>G synonymous_variant 0.15
rpoC 764581 c.1212T>C synonymous_variant 0.16
rpoC 764582 p.Leu405Met missense_variant 0.16
rpoC 764593 c.1224C>T synonymous_variant 0.21
rpoC 764602 c.1233C>T synonymous_variant 0.21
rpoC 764605 c.1236G>T synonymous_variant 0.21
rpoC 764611 c.1242G>T synonymous_variant 0.22
rpoC 764626 c.1257C>T synonymous_variant 0.2
rpoC 764632 c.1263T>C synonymous_variant 0.18
rpoC 764647 c.1278C>T synonymous_variant 0.13
rpoC 764650 c.1281G>C synonymous_variant 0.11
rpoC 764656 c.1287C>T synonymous_variant 0.12
rpoC 764662 c.1293G>C synonymous_variant 0.13
rpoC 764677 c.1308C>G synonymous_variant 0.13
rpoC 764678 p.Lys437Gln missense_variant 0.13
rpoC 764706 p.Leu446Gln missense_variant 0.12
rpoC 764713 c.1344G>T synonymous_variant 0.12
rpoC 764731 c.1362G>C synonymous_variant 0.12
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.5
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.5
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.15
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.23
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.65
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.19
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.19
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.59
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.61
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.59
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.87
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.57
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.6
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.3
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.59
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.74
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.29
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.29
rrs 1472290 n.445C>G non_coding_transcript_exon_variant 0.29
rrs 1472293 n.448C>A non_coding_transcript_exon_variant 0.29
rrs 1472297 n.453_461delGTCCGGGTT non_coding_transcript_exon_variant 0.29
rrs 1472309 n.464C>T non_coding_transcript_exon_variant 0.29
rrs 1472311 n.466C>T non_coding_transcript_exon_variant 0.29
rrs 1472312 n.468_470delGAT non_coding_transcript_exon_variant 0.25
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 0.25
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 0.25
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.25
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.29
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.25
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.15
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.31
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.36
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.44
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.44
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.44
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.44
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.25
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.5
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.5
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.36
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.18
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.62
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.2
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.52
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.52
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.31
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.31
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.94
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.88
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.66
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.31
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.64
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.57
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.29
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.88
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.85
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.93
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.85
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.29
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.55
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.31
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.6
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.31
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.6
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.57
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.58
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.47
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.3
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.3
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.22
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.22
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.59
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.5
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.32
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.5
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.82
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.88
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.67
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.54
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.5
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.84
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.32
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.4
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.93
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.93
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.93
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.89
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.5
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.52
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.85
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.83
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.8
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.71
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.8
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.81
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.81
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.22
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.81
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.61
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.62
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.87
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.86
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.76
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.76
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.85
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.93
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.94
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.93
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.9
rrs 1473293 n.1449delA non_coding_transcript_exon_variant 0.87
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.86
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.88
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.86
rrl 1473384 n.-274A>G upstream_gene_variant 0.57
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.33
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.21
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.67
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.25
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.25
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.5
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.67
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.5
rrl 1475768 n.2112T>C non_coding_transcript_exon_variant 0.57
rrl 1475768 n.2110_2111insT non_coding_transcript_exon_variant 0.73
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.24
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.56
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.12
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.15
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.75
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.79
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.62
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.69
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.69
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.69
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.15
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.23
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.85
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.83
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.7
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.7
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.6
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.7
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.78
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.78
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.78
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.71
rrl 1475995 n.2338G>C non_coding_transcript_exon_variant 0.6
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.27
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.91
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.9
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.93
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.6
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.82
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.9
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.86
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.75
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.36
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.5
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.22
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.38
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.5
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.67
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.57
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.38
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.62
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.5
rrl 1476542 n.2885T>C non_coding_transcript_exon_variant 0.25
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.38
rpsA 1834069 c.528G>C synonymous_variant 0.1
rpsA 1834249 c.708T>C synonymous_variant 0.12
rpsA 1834294 c.753G>C synonymous_variant 0.18
rpsA 1834298 p.Gln253Glu missense_variant 0.19
rpsA 1834306 c.765T>C synonymous_variant 0.2
rpsA 1834307 p.Asp256Gln missense_variant 0.2
rpsA 1834312 c.771G>A synonymous_variant 0.19
rpsA 1834327 c.786G>T synonymous_variant 0.17
rpsA 1834345 c.804C>T synonymous_variant 0.14
rpsA 1834348 c.807T>C synonymous_variant 0.17
rpsA 1834354 c.813G>C synonymous_variant 0.15
rpsA 1834357 c.816T>C synonymous_variant 0.12
rpsA 1834360 c.819G>C synonymous_variant 0.11
rpsA 1834361 c.820T>C synonymous_variant 0.14
rpsA 1834366 c.825A>G synonymous_variant 0.12
rpsA 1834375 c.834G>C synonymous_variant 0.17
rpsA 1834378 c.837T>C synonymous_variant 0.13
rpsA 1834387 c.846C>T synonymous_variant 0.17
rpsA 1834411 c.870T>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 2223117 c.48C>T synonymous_variant 0.15
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
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859846 p.Glu191Asp missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 1.0
clpC1 4039547 c.1131_1157delGGCGATGGTGGCCGCCGCGACCCTGGC disruptive_inframe_deletion 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244350 p.Leu373Pro missense_variant 1.0
embA 4244800 p.Val523Glu missense_variant 0.2
aftB 4267146 p.Ala564Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0