Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,403,597	0	T	C	45.6%	12.3 / 67.1	57	intergenic (‑57/+24)	PP_1227/PP_1228	membrane protein/methyl‑accepting chemotaxis transducer
Reads supporting (aligned to +/- strand):  ref base T (17/14);  new base C (12/14);  total (29/28)
Fisher's exact test for biased strand distribution p-value = 5.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.18e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TGAACAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGAATGCC  >  NC_002947/1403456‑1403740                                                                                                                                              |                                                                                                                                                tGAACAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGa                                                                                                                                         <  2:2722472/150‑1 (MQ=255)  gAACAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGaa                                                                                                                                        <  1:2603667/150‑1 (MQ=255)  gAACAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGaa                                                                                                                                        <  2:356964/150‑1 (MQ=255)  gAACAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGaa                                                                                                                                        <  1:1536359/150‑1 (MQ=255)   aaCAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAag                                                                                                                                       <  2:703103/150‑1 (MQ=255)    aCAGGGTGGCGGCGATCGAGGTGCGTAAAAGCTCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAaga                                                                                                                                      <  2:2194031/150‑1 (MQ=255)    aCAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAaga                                                                                                                                      <  1:1214139/150‑1 (MQ=255)    aCAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAaga                                                                                                                                      <  2:2677307/150‑1 (MQ=255)    aCAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGAaga                                                                                                                                      <  1:1864171/150‑1 (MQ=255)    aCAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGAaga                                                                                                                                      <  1:1651233/150‑1 (MQ=255)     cAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAagag                                                                                                                                     <  2:1413544/150‑1 (MQ=255)     cAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGAagag                                                                                                                                     <  1:1105825/150‑1 (MQ=255)      aGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAgg                                                                                                                                    <  2:2377732/150‑1 (MQ=255)          gggcggcGATCGGGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTACGCATTAGTTGTGCTCAAGCATGCCGATGGGGCGGTTGCTGTCAGGGGCTCTTGGCGGGCACGCCAGCTAAGGGGCCCt                                                                                                                                <  2:1504429/149‑1 (MQ=255)                                aaGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGAc                                                                                                                             <  2:13211/131‑1 (MQ=255)                                aaGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGAc                                                                                                                             >  1:13211/1‑131 (MQ=255)                                  gCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGAagag                                                                                                                                     <  1:395762/121‑1 (MQ=255)                                  gCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCAGAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGAagag                                                                                                                                     >  2:395762/1‑121 (MQ=255)                                                  gATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCctgctgc                                                                                        >  1:138167/1‑150 (MQ=255)                                                                                    aTAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGaa                                                                                                                                        >  1:2160464/1‑68 (MQ=255)                                                                                    aTAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGaa                                                                                                                                        <  2:2160464/68‑1 (MQ=255)                                                                                     tAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCg                                                     >  1:1944657/1‑150 (MQ=255)                                                                                            tgCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGAt                                              >  2:2305331/1‑150 (MQ=255)                                                                                               tCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTc                                                                                                        <  1:242271/89‑1 (MQ=255)                                                                                               tCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTc                                                                                                        >  2:242271/1‑89 (MQ=255)                                                                                                                        tGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGccc                                <  2:2739744/136‑1 (MQ=255)                                                                                                                        tGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGccc                                >  1:2739744/1‑136 (MQ=255)                                                                                                                            aGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCAc              >  2:2335286/1‑150 (MQ=255)                                                                                                                             gggCCTCTTCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACg             >  1:1129814/1‑150 (MQ=255)                                                                                                                              ggCCTCTTCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGt                                                    <  1:485927/110‑1 (MQ=255)                                                                                                                              ggCCTCTTCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGt                                                    >  2:485927/1‑110 (MQ=255)                                                                                                                                ccTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGt                                                    <  1:1867953/108‑1 (MQ=255)                                                                                                                                ccTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGt                                                    >  2:1867953/1‑108 (MQ=255)                                                                                                                                ccTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGATTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGtct          <  1:2305331/150‑1 (MQ=255)                                                                                                                                ccTCTTCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGAAAGCGCAGTTTTTTATTCTGTCACGtct          >  2:2043684/1‑150 (MQ=37)                                                                                                                                 ctctTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGtctc         >  2:2509703/1‑150 (MQ=255)                                                                                                                                 ctctTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGtctc         >  1:924229/1‑150 (MQ=255)                                                                                                                                 ctctTCGCGGGCACGCCCGCGAAGAGTCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGtctc         >  2:1953170/1‑150 (MQ=255)                                                                                                                                 ctctTCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCctgctgctg                                                                                      <  1:1711005/73‑1 (MQ=255)                                                                                                                                 ctctTCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCctgctgctg                                                                                      >  2:1711005/1‑73 (MQ=255)                                                                                                                                  tctTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCg        >  2:988269/1‑150 (MQ=255)                                                                                                                                  tctTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCg        >  2:1293278/1‑150 (MQ=255)                                                                                                                                  tctTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGGTATTCTGTGACGTCTCg        >  1:1277502/1‑150 (MQ=255)                                                                                                                                  tctTCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCg        >  2:2630013/1‑150 (MQ=255)                                                                                                                                  tctTCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCg        >  1:1194339/1‑150 (MQ=255)                                                                                                                                    ttCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTgg                                                             >  2:2363267/1‑95 (MQ=255)                                                                                                                                    ttCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTgg                                                             <  1:2363267/95‑1 (MQ=255)                                                                                                                                    ttCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCAt                                                                                                     >  1:635101/1‑55 (MQ=18)                                                                                                                                    ttCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCAt                                                                                                     <  2:635101/55‑1 (MQ=18)                                                                                                                                    ttCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTTCCGATTCATCGGCCTGCCCAGCCAGTGCTTCTGTCACGTCTCGaa      >  1:2367607/1‑150 (MQ=255)                                                                                                                                    ttCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCg                                        <  2:1867875/116‑1 (MQ=255)                                                                                                                                    ttCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCg                                        >  1:1867875/1‑116 (MQ=255)                                                                                                                                    ttCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGaa      >  2:915032/1‑150 (MQ=255)                                                                                                                                      cgcgGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGAATg    <  1:2630013/150‑1 (MQ=255)                                                                                                                                        cgGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGAATGcc  >  1:717277/1‑150 (MQ=255)                                                                                                                                         gggCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTc                <  1:1507571/135‑1 (MQ=255)                                                                                                                                         gggCGTGCCCGCGAAGAGGCCATGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTc                >  2:1507571/1‑135 (MQ=255)                                                                                                                                              |                                                                                                                                                TGAACAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGAATGCC  >  NC_002947/1403456‑1403740

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑