Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,781,645	0	A	C	50.0%	69.8 / 15.2	56	V361G (GTT→GGT)	ypjA	adhesin‑like autotransporter
Reads supporting (aligned to +/- strand):  ref base A (23/5);  new base C (0/28);  total (23/33)
Fisher's exact test for biased strand distribution p-value = 6.21e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGATATAATTGTTGTGTCAGCTTTCCCGCCGCTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTCCAGCAACACATTGTCT  >  NC_000913/2781497‑2781788                                                                                                                                                       |                                                                                                                                                ggaTATAATTGTTGTGTCAGCTTTCCCGCCGCTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAAcc                                                                                                                                               >  1:416578/1‑151 (MQ=255)           gttgtGTCAGCTTTCCCGCCGCTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCTATAACCCCGCCATTAt                                                                                                                                     >  1:713775/1‑151 (MQ=255)               tgtCAGCTTTCCCGCCGCTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTAt                                                                                                                                 >  1:67494/1‑151 (MQ=255)               tgccattttccccGCCTTTTTTGATATTTTGCGTTCCGCTGTTGATATGGGTGCTTGTGGTTATGCCATAATTATTAATTTTCTGTGTCCCACAATTAATTATGTTTTTTGTCGCTTTT‑CCTGCAAC‑ACCCAAACCCCCGCCATTATCt                                                                                                                                   <  1:372753/139‑1 (MQ=255)                ggctgtttccccGCCTTTTTTGATATTTGGCGTTCCGCTGTTGATTTTGGTCCCTGTGGTTATGCCATAATTATTAATATTCTGTGTCCCACCATTAATTATGGTTTTTGTCGCTTTT‑CCTGCAAC‑ACCCATAACCCCGCCATTATCTAtt                                                                                                                                <  1:303792/142‑1 (MQ=255)                     cTTTCCCGCCGCTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGt                                                                                                                           >  1:947408/1‑151 (MQ=255)                          ccgcctTTTTTGTTATTTTGCTTTCCGTTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTCCCACCATTAATTATGTTTTTTGTCGCGTTT‑CCTGCAAC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCAt                                                                                                                      <  1:500091/151‑1 (MQ=255)                             ccgcTTTTGATTTTTTGCTTTCGGTTGTTGATTTTGGTGCCTGTGGCTATGCAATATTTATTAATATTTTGTGTGCCCCCATTAATTAGGTTTTTTGTCGCTTTT‑CTGGCAAC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAg                                                                                                                   <  2:836715/151‑1 (MQ=255)                                 ttttGATATTTTGCGTTCCGTTTTTGATATTGGTGCCTGTGGTTATGCCATAATTATAAATTTTCTGTGTCCCCCCATTATTTATGGTTTTTGTCGCTTTC‑CCTCAAAC‑ACCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCt                                                                                                                 <  1:701650/149‑1 (MQ=255)                                  tttGATATTTTGCGTCCCGCTTTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGTCGCTTTT‑CCTGCAAC‑ATCCAAACCCCCGCCATTATCTATTCGGGTCGCATCAGCttt                                                                                                               <  2:712433/150‑1 (MQ=255)                                      atatTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCAt                                                                                                          >  1:45973/1‑151 (MQ=255)                                       ttttttGCTTTCCGTTGTTGATATTGGTCCCTGTGGCTATGCCATAATTATTAATATTTTGTGTCCCCCCATAAATTTTGTTTTTTGTCGCTTTT‑CCTCAAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGc                                                                                                            <  1:348764/146‑1 (MQ=255)                                         ttttGCTTCCCGCTGTTGATATTGGTGCCTGTGGCTATGCAATAATTATAAATATTCTGTGTCCCACCATTAATTATGTTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCAtt                                                                                                         <  2:828152/149‑1 (MQ=255)                                                ttcctgttttatatttGGTCCTTTTGGTTTTGCTATAATTATAAATTTTTTGTGTCCCCCAATTAATTATGTTTTTTTTCG‑GTTT‑CCTTCCACTTTCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTaaa                                                                                                  <  1:790514/135‑1 (MQ=255)                                                ttCCGCTGTTGATATTGGTGCCTGTGGCTATGCAATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGTCGGGTTC‑CCTGCAAC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTaaa                                                                                                  <  1:801895/149‑1 (MQ=255)                                                 tCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGAATTTGTCGCGTTT‑CCTCCAAC‑ATACATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACt                                                                                               >  1:904512/1‑151 (MQ=255)                                                      tGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACAt                                                                                          >  1:464008/1‑151 (MQ=255)                                                        ttGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTg                                                                                        >  1:305778/1‑151 (MQ=255)                                                           atatTGGTGCCTGGGGCTATGCCATAATTATTAATATTCTGTGTGCCCCCATTAATTATGGTATTTGTCGCGTTC‑CCTGAAAC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGtt                                                                                      <  2:561497/150‑1 (MQ=255)                                                            tatTGGGGCCTGTGTCTTTGCCATAATTATTAATATTCTGTGTGCCACAATTAATTATGGTTTTTGTCGCTTTT‑CCTGAAAC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGt                                                                                       <  1:535485/148‑1 (MQ=255)                                                              tgggtccttttgGCTATCCAATATTTATTAATTTTTTGTGTGCCACAATTATTTATGTTTTTTGTCGTTTTC‑CCTCCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCt                                                                                   <  1:737119/140‑1 (MQ=255)                                                               tGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCttt                                                                                 >  2:508098/1‑151 (MQ=255)                                                                 gtgcgtgctgttagtccATAATGATCAATCCTCTTTGTGCCACAATTAATTATTGTTTTTGGC‑CGTTTCCCAGCACC‑ACCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTAt                                                                               <  2:752144/136‑1 (MQ=255)                                                                       gtgGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTATTTATGTTTTTTGTCGCTTTT‑CCTGCAAC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTta                                                                          <  2:23878/150‑1 (MQ=255)                                                                         ggttttGCAATAATTATTAATATTCTGTGTGCCACCATTAATTATGTTTTTTGTCGCTTTT‑CCTGCAAC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTtaata                                                                       <  2:607931/146‑1 (MQ=255)                                                                         ggttATGCCATATTTATTAATTTTCTGTGTCCCACCATAAATTATGTTATTTGTCGCGTTT‑CCTCCAAC‑ATCAATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCttt                                                                           <  1:836537/144‑1 (MQ=255)                                                                                ccATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCt                                                                >  2:530480/1‑151 (MQ=255)                                                                                ccATAATTATTAATATTCTGTGTCCCTCAATTATTTATGGTTTTGGTCGCTTTT‑CCTGAACC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTc                                                                 <  1:906914/150‑1 (MQ=255)                                                                                  aTAATTTTTAATATTTTGTTACCCCAAATAAATTATGTTATGTCTCGCGTTC‑CCTACAAC‑TCCCATAACACCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCtt                                                               <  1:568531/150‑1 (MQ=255)                                                                                    atttattaATATTTTGTGTGCCACCATTAATTATGGTTTTTGTCGCTTTT‑CCTGCAAC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCt                                                                <  2:1044458/145‑1 (MQ=255)                                                                                           aaTTTTCTGTGTCCCACCATTAATTATGTTTTTTGTCGCTTTT‑CCTGAAAC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCg                                                       <  1:689724/149‑1 (MQ=255)                                                                                           aaTATTCTGTGTGCCCCCATTAATTATGGTATTTGTCGCTTTC‑CCTGCAAC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGa                                                      <  2:540388/150‑1 (MQ=255)                                                                                               ttCTGTGTGCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ACCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCa                                                  <  2:88456/150‑1 (MQ=255)                                                                                                   gtgtgCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGc                                             >  1:778028/1‑151 (MQ=255)                                                                                                    tgtgCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCg                                            >  2:78387/1‑151 (MQ=255)                                                                                                     gcgCCCCCATTATTTATGTTATTTGTCGCGTTC‑CCTGAAAC‑ACCCAAACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATg                                              <  2:526794/146‑1 (MQ=255)                                                                                                         caccaTTAATTATGTTTTTTGTCGCTTTT‑CCTGAAAC‑AACCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTAt                                       <  1:526318/151‑1 (MQ=255)                                                                                                             attaattaTGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCt                                   >  2:516032/1‑151 (MQ=255)                                                                                                              ttatttatGTTTTTTGTCGCTTTT‑CCTGCACC‑TTCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCt                                   <  1:46893/150‑1 (MQ=255)                                                                                                              ttaattaTGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCTCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCt                                   >  1:241542/1‑150 (MQ=255)                                                                                                               taattaTGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGACATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTa                                  >  1:340474/1‑150 (MQ=255)                                                                                                                   taTGGTTTTTGTCGCTTTT‑CCTCCAAC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATg                              <  1:154501/150‑1 (MQ=255)                                                                                                                        tATTTGTCGCGTTT‑CCTGCAAC‑ACCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGaccac                         <  2:550937/150‑1 (MQ=255)                                                                                                                         aTTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCg                       >  2:491003/1‑151 (MQ=255)                                                                                                                         aTTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCg                       >  1:729289/1‑151 (MQ=255)                                                                                                                           tttccgtgTTT‑CCTAAAAC‑TCCCAAACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGaccacc                        <  1:549447/141‑1 (MQ=255)                                                                                                                           ttGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGtt                     >  1:1016881/1‑151 (MQ=255)                                                                                                                               cgcgTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTcc                 >  1:771472/1‑151 (MQ=255)                                                                                                                                   ttt‑CCTGCAAC‑ACCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGttt                    <  2:684859/144‑1 (MQ=255)                                                                                                                                    ttcccTCCACC‑ATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGttt                    <  1:957312/141‑1 (MQ=255)                                                                                                                                        cTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTCCAGCAacac         >  2:1026365/1‑151 (MQ=255)                                                                                                                                          gCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTCCAGCAACACAt       >  2:610203/1‑151 (MQ=255)                                                                                                                                          gCAAC‑ACCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTCCAGCAacac         <  2:588758/149‑1 (MQ=255)                                                                                                                                                aTCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTCCAGCAACACATTGTCt  <  2:71059/151‑1 (MQ=255)                                                                                                                                                aTCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTCCAGCAACACATTGTCt  >  2:389058/1‑151 (MQ=255)                                                                                                                                                aTCCATAACACCGCCATTATCTATTCGGTTCGCATCAGATTTAGAATTGGTTAAAACTGACATTGTTCCTTTATCTTTTATAATTGTCTTGATTGCCGAACCATCTTCGTTTATTTCTAAATGACCACCGTTTTGCAGCAACACATTGTCt  >  1:705405/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                GGATATAATTGTTGTGTCAGCTTTCCCGCCGCTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGTCGCGTTT‑CCTGCAAC‑ATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTCCAGCAACACATTGTCT  >  NC_000913/2781497‑2781788

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑