Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	753,125	0	T	A	24.5%	108.1 / 15.6	49	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
Reads supporting (aligned to +/- strand):  ref base T (31/6);  new base A (0/12);  total (31/18)
Fisher's exact test for biased strand distribution p-value = 2.01e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

ATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCG  >  NC_000913/752991‑753263                                                                                                                                       |                                                                                                                                            ataAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATaaaaa                                                                                                                                        >  2:269052/1‑140 (MQ=255)       gCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAAcc                                                                                                                                  >  1:716794/1‑140 (MQ=255)       gCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAAcc                                                                                                                                  >  2:428660/1‑140 (MQ=255)         gACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCg                                                                                                                                >  1:1036387/1‑140 (MQ=255)                     ttttttAATTAAAAGTTTTGGGTTGCTGATAATTTGAGTTTTTTTTTTTTTTTTAAATATCTATATAGGTTTGTAAATGGTTTTTTTTTTTACATTTTTTTGTTTTTAGGCATAAAAAAATCAACCCGCCATATGAAcgg                                                                                                                    <  2:1026725/139‑1 (MQ=255)                                              cTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGc                                                                                          >  1:1071920/1‑140 (MQ=255)                                                  aattttGAGCTTTTTTTTTTTTTTTAAATTTTTATATAGGTCTTTTAATGGTTTTTTTTTTTACATTTTTTTGTTTTTAGGCATAAAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATc                                                                                      <  2:918740/137‑1 (MQ=255)                                                              ttCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGc                                                                          >  1:918740/1‑140 (MQ=255)                                                                   ttCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGat                                                                     >  1:255419/1‑140 (MQ=255)                                                                      tttttAAATTTTTATATAGCTCTATTAATAGATTTTATTTTAACATTTTTTTGTGTTGAGATATAAAAAATTTACCCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATc                                                                  <  2:716794/140‑1 (MQ=255)                                                                        tttAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGc                                                                >  1:872228/1‑140 (MQ=255)                                                                        tttAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGc                                                                >  2:324988/1‑140 (MQ=255)                                                                        tttAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAAACATTAAGCCTTGAGATTGc                                                                >  2:1154142/1‑140 (MQ=255)                                                                        tttAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAAACACTAACGCTTGGTATccc                                                                >  1:548087/1‑138 (MQ=255)                                                                                tCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAg                                                        >  1:1139086/1‑140 (MQ=255)                                                                                      tgggTCTTTTAATGTATTTTTTTTTTACAATTTTTTGTGTTTAGGCATAAAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGt                                                  <  1:96541/138‑1 (MQ=255)                                                                                      taGTTCTTTTAATGTTTTTTATTTTTACATTTTTTTTTTTTTAGAAATAAAAAAACCACCCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTTAAGTCGCGt                                                  <  2:255419/140‑1 (MQ=255)                                                                                      taGGTCTGTTAATGGTTTTTTTTTTTACATTTTTTTGTTTTTAGGAATAAAAAAACCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGt                                                  <  1:428660/140‑1 (MQ=255)                                                                                         gTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGCTTAAACTA‑TTACAAATTAACAAACCATCATTTACGCTTGTGTTCGCTTTTAAACTcacagctt                                               >  2:301649/1‑133 (MQ=255)                                                                                         gTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGtttt                                               >  1:333673/1‑140 (MQ=255)                                                                                         gTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGtttt                                               >  1:552512/1‑140 (MQ=255)                                                                                         gTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGtttt                                               >  1:92627/1‑140 (MQ=255)                                                                                           cTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTc                                             >  1:890751/1‑140 (MQ=255)                                                                                            tGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTc                                             <  1:1059587/139‑1 (MQ=255)                                                                                            tGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTc                                             >  2:1059587/1‑139 (MQ=255)                                                                                            tGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCa                                            >  1:675219/1‑140 (MQ=255)                                                                                            tGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCa                                            >  1:118020/1‑140 (MQ=255)                                                                                            tGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAACAATCAACCATTAACGCTTGATATCGCTTTTTAAAACGCGTTTTTCa                                            >  2:573331/1‑140 (MQ=255)                                                                                             tttAATGTTTTTTATTTTTAAATTTTTTTGTGTTTAGGCATAAAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCat                                           <  2:1139086/139‑1 (MQ=255)                                                                                             tttAATGGTTTTTTTTTTTACATTTTTTTGTGTTTAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCat                                           <  1:573331/139‑1 (MQ=255)                                                                                             tttAATGGTTTTTTTTTTTAAATTTTTTTGTTTTTAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCat                                           <  2:1022776/139‑1 (MQ=255)                                                                                             tttAATGGATTTTTTTTTTACAATTTTTTGTGTTTAGGAATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCat                                           <  1:338204/139‑1 (MQ=255)                                                                                             tttAATGGATTTTATTTTTACAATTTTTTGTTTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCat                                           <  1:335412/139‑1 (MQ=255)                                                                                             tttAATGATTTTTATTTTTACATTTTTTTGTTTTTAGGCATAAAAAAACCACCCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCat                                           <  2:675219/139‑1 (MQ=255)                                                                                              ttAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCata                                          >  1:1070980/1‑140 (MQ=255)                                                                                              ttAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCata                                          >  1:914838/1‑140 (MQ=255)                                                                                              ttAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCata                                          >  1:258799/1‑140 (MQ=255)                                                                                              ttAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCata                                          >  1:818663/1‑140 (MQ=255)                                                                                              ttAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAATCGCGTTTTTCata                                          >  1:564029/1‑140 (MQ=255)                                                                                              ttAATGGATTTCATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTTCAACTTTACAAATCACCATTTACCCATGATATCTCTTTTTAAGTCGCGTTTTTCata                                          >  2:744411/1‑140 (MQ=255)                                                                                                actgtatttttttttTACAATTTTTTGTCTTTTGAAAAATAAAAAAAAATCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATc                                        <  2:548087/135‑1 (MQ=255)                                                                                                aaTGGTTTTTTTTTTTACATTTTTTTGTGTTTAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATc                                        <  1:1171327/140‑1 (MQ=255)                                                                                                aaTGGTTTTTTTTTTTAAATTTTTTTGTTTTTAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATc                                        <  2:460893/140‑1 (MQ=255)                                                                                                aaTGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATc                                        >  2:539205/1‑140 (MQ=255)                                                                                                   ggATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTg                                     >  1:388333/1‑140 (MQ=255)                                                                                                     tttttttttttACATTTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGta                                   <  1:602857/139‑1 (MQ=255)                                                                                                     tttttttttttACATTTTTTTGTGTTTAGGAAAAAAAAAACCACCCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGta                                   <  2:1071920/139‑1 (MQ=255)                                                                                                        ttattttTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTTCAACTTAACAATCAAACATTAACGCCTGATATCGCTTTTAAAGACGCGTTTTTCATATCCCGTATAc                                >  2:238633/1‑140 (MQ=255)                                                                                                                  atttttttGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGAcgcg                      <  1:324988/138‑1 (MQ=255)                                                                                                                       tttttttttAGGCATAAAAAAACCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACgg                 <  2:818663/134‑1 (MQ=255)                                                                                                                         tgttTTTAGTCAAAAAAAACCCAACCCGCCATATGAACGGCGGG‑TTAAAATATTCACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGc               <  2:240268/140‑1 (MQ=255)                                                                                                                            ttttAGGAATAAAAAAACCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAAt            <  2:872228/139‑1 (MQ=255)                                                                                                                               tAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCtt         >  2:833318/1‑140 (MQ=255)                                                                                                                                 ggCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCa       <  2:914838/140‑1 (MQ=255)                                                                                                                                 ggCATAAAAAAATCACCCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCa       <  1:339365/140‑1 (MQ=255)                                                                                                                                    atatAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATAc    <  2:92627/140‑1 (MQ=255)                                                                                                                                      ataAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCg  <  1:539205/140‑1 (MQ=255)                                                                                                                                       taAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCg  >  1:194282/1‑139 (MQ=255)                                                                                                                                       taAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCg  <  2:194282/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                            ATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGG‑TTAAAATATTTACAACTTAGCAATCAACCATTAACGCTTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCG  >  NC_000913/752991‑753263

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑