breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 298 shown)
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,165,9680CT56.4% 217.0 / inf 550intergenic (+283/‑117)ycfP/ndhputative UPF0227 family esterase/respiratory NADH dehydrogenase 2/cupric reductase
*NC_0009132,704,1030GT53.4% 41.0 / inf 537intergenic (‑40/+232)rnc/lepBRNase III/leader peptidase (signal peptidase I)
*NC_0009131,828,6590GA52.6% 35.8 / inf 484T359M (ACG→ATG) astDsuccinylglutamic semialdehyde dehydrogenase
*NC_0009134,530,7970CT49.4% 52.6 / inf 479Q285Q (CAG→CAAsgcXputative endoglucanase with Zn‑dependent exopeptidase domain
*NC_0009134,571,2800CT48.5% 101.6 / inf 497E99K (GAG→AAG) yjiRputative DNA‑binding transcriptional regulator/putative aminotransferase
*NC_0009133,256,1570CT48.4% 109.8 / inf 487Q165Q (CAG→CAAyhaMputative L‑serine dehydratase alpha chain
*NC_0009134,337,8640CT48.3% 129.3 / inf 578V22V (GTG→GTAadiYadi system transcriptional activator
*NC_000913312,8650GA48.2% 109.4 / inf 531intergenic (‑88/+276)ykgM/ykgR50S ribosomal protein L31 type B; alternative zinc‑limitation L31 protein/uncharacterized protein
*NC_0009133,588,7870GA48.2% 115.9 / inf 505P132S (CCG→TCG) ugpCsn‑glycerol‑3‑phosphate ABC transporter ATPase
*NC_000913466,1480GA47.9% 126.8 / inf 510P389S (CCA→TCA) ybaEputative ABC transporter periplasmic binding protein
*NC_0009132,046,5060GT47.8% 159.4 / inf 461V523V (GTG→GTTyeeJputative adhesin
*NC_0009134,435,7500CT47.8% 110.2 / inf 452G272G (GGG→GGAcpdB2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase
*NC_0009131,322,7590GA47.8% 120.2 / inf 450A63V (GCT→GTT) trpEcomponent I of anthranilate synthase
*NC_0009134,359,9090CT47.7% 101.2 / inf 528W41* (TGG→TGAcadBputative lysine/cadaverine transporter
*NC_0009133,259,2830GA47.7% 119.8 / inf 524H123Y (CAT→TAT) tdcGL‑serine dehydratase 3, anaerobic
*NC_0009133,559,6210CT47.4% 110.5 / inf 434P452S (CCC→TCC) rtcRsigma 54‑dependent transcriptional regulator of rtcBA expression
*NC_0009132,085,3190GA47.4% 106.1 / inf 448A69A (GCC→GCTyeeEUPF0394 family inner membrane protein
*NC_0009134,553,6710CT47.4% 137.0 / inf 464F257F (TTC→TTTuxuBD‑mannonate oxidoreductase, NAD‑dependent
*NC_000913469,2710GA47.3% 126.3 / inf 473G134E (GGG→GAG) mdlAputative multidrug ABC transporter ATPase
*NC_0009134,234,4790CT47.3% 137.2 / inf 496A241V (GCG→GTG) pgiglucosephosphate isomerase

Marginal new junction evidence (lowest skew 10 of 104 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1978503 =NA (NA)275 (0.540) 170/300 3.3 NA noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 4434636 NA (NA)coding (1930/1944 nt) cpdB 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase
* ? NC_000913 = 1095502NA (NA)268 (0.530) 164/298 3.9 44.4% noncoding (1/1258 nt) IS3 repeat region
?NC_000913 = 1199871 335 (0.660)coding (936/1128 nt) intE e14 prophage; putative integrase
* ? NC_000913 = 1050545NA (NA)255 (0.510) 162/296 4.0 NA noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 4434636 NA (NA)coding (1930/1944 nt) cpdB 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase
* ? NC_000913 315229 =NA (NA)274 (0.550)
+TC
162/296 4.0 44.7% noncoding (1/1255 nt) IS3 repeat region
?NC_000913 = 1199872 343 (0.670)coding (935/1128 nt) intE e14 prophage; putative integrase
* ? NC_000913 273955 =NA (NA)355 (0.700) 164/300 4.0 51.4% noncoding (1195/1195 nt) IS5 repeat region
?NC_000913 = 565828 336 (0.660)coding (151/1164 nt) intD DLP12 prophage; putative phage integrase
* ? NC_000913 = 275149NA (NA)256 (0.500) 161/300 4.4 41.9% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 295082 = 355 (0.700)intergenic (‑283/+57) yagM/yagN CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein
* ? NC_000913 = 4020781258 (0.510)240 (0.470) 160/300 4.5 48.1% coding (556/1641 nt) ubiB regulator of octaprenylphenol hydroxylation, ubiquinone synthesis; regulator of 2'‑N‑acetyltransferase; putative ABC1 family protein kinase
?NC_000913 4020794 = 260 (0.510)coding (569/1641 nt) ubiB regulator of octaprenylphenol hydroxylation, ubiquinone synthesis; regulator of 2'‑N‑acetyltransferase; putative ABC1 family protein kinase
* ? NC_000913 1909925 =321 (0.640)388 (0.770) 159/298 4.5 54.7% coding (175/792 nt) kdgR KDG regulon transcriptional repressor
?NC_000913 2101749 = NA (NA)noncoding (1195/1195 nt) IS5 repeat region
* ? NC_000913 257908 =NA (NA)250 (0.490) 160/300 4.5 46.6% noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 1907403 287 (0.560)coding (33/210 nt) cspC stress protein, member of the CspA‑family
* ? NC_000913 1094245 =NA (NA)234 (0.460) 159/300 4.7 40.0% noncoding (1258/1258 nt) IS3 repeat region
?NC_000913 1199869 = 351 (0.690)coding (938/1128 nt) intE e14 prophage; putative integrase