Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,424,935	T→A	8.5%	intergenic (+480/‑32)	PP_3039 → / → PP_3040	hypothetical protein/holin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,424,935	0	T	A	8.5%	179.5 / 7.4	59	intergenic (+480/‑32)	PP_3039/PP_3040	hypothetical protein/holin
Reads supporting (aligned to +/- strand):  ref base T (26/28);  new base A (2/3);  total (28/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.57e-01

AACAGACATTCCCCGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATGGCCGGCGTT  >  NC_002947/3424789‑3425077                                                                                                                                                    |                                                                                                                                               aaCAGACATTCCCCGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGgc                                                                                                                                             >  2:180656/1‑150 (MQ=255)  aCAGACATTCCCCGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGgcg                                                                                                                                            >  1:887972/1‑150 (MQ=255)   cAGACATTCCCCGGACGTTTACCACTTATTGCAGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGAACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGgcgc                                                                                                                                           >  2:1151939/1‑150 (MQ=255)      aCATTCCCCGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCgg                                                                                                                                        <  1:180656/150‑1 (MQ=255)            cccGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGAGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGtttt                                                                                                                                  <  2:834860/150‑1 (MQ=255)             ccGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCGCCAGG‑GCCGGGGttttc                                                                                                                                 <  1:696822/150‑2 (MQ=255)                    tttACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTg                                                                                                                          <  1:1011962/150‑1 (MQ=255)                     ttACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTgg                                                                                                                         <  2:552143/150‑1 (MQ=255)                      tACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTggg                                                                                                                        <  1:1198390/150‑1 (MQ=255)                        ccACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTggggg                                                                                                                      >  2:891900/1‑150 (MQ=255)                            ttATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTc                                                                                                                  <  1:59042/150‑1 (MQ=255)                                  ccGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCAAGGC‑CCTTGCGCCGGGGTTTTTTCCTTTGGGGGATTCGATGaa                                                                                                            >  2:96526/1‑150 (MQ=255)                                    gggTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCAGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACa                                                                                                          <  2:315904/150‑1 (MQ=255)                                       tGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAgtg                                                                                                       >  2:82628/1‑148 (MQ=255)                                          cATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGagc                                                                                                    >  1:855022/1‑150 (MQ=255)                                           aTTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCGCCAGG‑GCCGGGGttttca                                                                                                                                <  1:856100/121‑3 (MQ=39)                                           aTTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCGCCAGG‑GCCGGGGttttca                                                                                                                                >  2:856100/1‑119 (MQ=39)                                           aTTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCGCCAGG‑GCCGGGGttt                                                                                                                                   <  2:650463/118‑1 (MQ=255)                                           aTTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGCGCCAGG‑GCCGGGGttt                                                                                                                                   >  1:650463/1‑118 (MQ=255)                                           aTTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCgg                                                                                                                                        <  2:239140/113‑1 (MQ=255)                                           aTTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCgg                                                                                                                                        >  1:239140/1‑113 (MQ=255)                                           aTTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGagca                                                                                                   >  1:805279/1‑150 (MQ=255)                                           aTTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGagca                                                                                                   >  1:902990/1‑150 (MQ=255)                                            ttAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCTCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGc                                                                                                        <  1:365391/144‑1 (MQ=255)                                            ttAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGc                                                                                                        >  2:365391/1‑144 (MQ=255)                                                aaCTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAg                                                                                              <  2:902990/150‑1 (MQ=255)                                                   tCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGtttt                                                                                                                                  >  2:534205/1‑111 (MQ=255)                                                   tCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGtttt                                                                                                                                  <  1:534205/111‑1 (MQ=255)                                                   tCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGt                                                                                           <  2:949273/150‑1 (MQ=255)                                                       ttGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCgg                                                                                                                                        >  2:466533/1‑101 (MQ=255)                                                       ttGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCgg                                                                                                                                        <  1:466533/101‑1 (MQ=255)                                                           tgcCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCACGCGTTAGTTgag                                                                                   >  2:397331/1‑150 (MQ=255)                                                             ccACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGAt                                                                                 <  2:790599/150‑1 (MQ=255)                                                               aCCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGt                                                                                           <  2:504170/138‑1 (MQ=255)                                                               aCCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGt                                                                                           >  1:504170/1‑138 (MQ=255)                                                               aCCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGc                                                                               <  2:887972/150‑1 (MQ=255)                                                                ccGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTg                                                                                                                          >  2:504965/1‑106 (MQ=255)                                                                ccGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTg                                                                                                                          <  1:504965/106‑1 (MQ=255)                                                                         aCCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCtggtt                                                                     >  1:152619/1‑150 (MQ=255)                                                                           cTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGACCAGGGAAATACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCtggttgg                                                                   <  2:1125373/150‑1 (MQ=255)                                                                                  aaGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGTGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCtt                                                            <  1:82628/150‑1 (MQ=255)                                                                                            cTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTg                                                  <  2:805279/150‑1 (MQ=255)                                                                                                    cGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTTCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGGCCATCTGGTTGGTGATCTTCCTGTCCCTGGTcggcgg                                          <  1:96526/150‑1 (MQ=255)                                                                                                       gCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGgt                                       <  2:855022/150‑1 (MQ=255)                                                                                                         gggCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGAt                                                                                                               <  2:97096/76‑1 (MQ=255)                                                                                                         gggCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGAt                                                                                                               >  1:97096/1‑76 (MQ=255)                                                                                                             gcACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGt                                                       <  2:722761/128‑1 (MQ=255)                                                                                                             gcACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGt                                                       >  1:722761/1‑128 (MQ=255)                                                                                                                caAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCga                              <  1:891900/150‑1 (MQ=255)                                                                                                                 aaaGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTggg                                                                                                                        <  2:487625/59‑1 (MQ=255)                                                                                                                 aaaGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTggg                                                                                                                        >  1:487625/1‑59 (MQ=255)                                                                                                                                   cTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATg           >  2:843468/1‑150 (MQ=255)                                                                                                                                    tGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGtt                                                                                      <  2:157770/74‑1 (MQ=255)                                                                                                                                    tGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGtt                                                                                      >  1:157770/1‑74 (MQ=255)                                                                                                                                    tGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATgg          >  1:712347/1‑150 (MQ=255)                                                                                                                                      aaaaCCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATGGcc        >  2:643378/1‑150 (MQ=255)                                                                                                                                           cccGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCt                                                                         >  2:177625/1‑80 (MQ=255)                                                                                                                                           cccGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCt                                                                         <  1:177625/80‑1 (MQ=255)                                                                                                                                            ccGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAAATGTTGCGGGGTGACATGGCCGGCGtt  >  2:579836/1‑150 (MQ=255)                                                                                                                                                    |                                                                                                                                               AACAGACATTCCCCGGACGTTTACCACTTATTGCCGGGTGGCATTAAAACTCGCTTGCTGCCACCGGAATCGACCTGTAAAAAGTACCCATCTTCGAGACGTGCGGGCGCACAAAGCGGCCCGCCAAACACTGAAAACCCCGGC‑CCTGGCGCCGGGGTTTTTGCCTTTGGGGGATTCGATGAACAGCGAGCAGCAAGCGTTAGTTGAGATGCCAATCTGGTTGGTGATCTTCCTGTCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATGGCCGGCGTT  >  NC_002947/3424789‑3425077

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: ‑