Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,560,996	G→T	22.0%	intergenic (+98/‑372)	yffL → / → yffM	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,560,996	0	G	T	22.0%	95.3 / 4.3	54	intergenic (+98/‑372)	yffL/yffM	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (23/18);  new base T (7/6);  total (30/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCC  >  NC_000913/2560854‑2561144                                                                                                                                               |                                                                                                                                                     tGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTAATAAGTTGCCGTTAAgg                                                                                                                                                >  5:45407/1‑149 (MQ=255)   cAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCTGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTg                                                                                                                                              <  2:403869/149‑1 (MQ=255)   cAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAATTTGCCGTAAAGTTg                                                                                                                                              >  3:226662/1‑149 (MQ=255)    aaCGAATACCAGTTATTATTCATGCCGTTCAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGTGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTgg                                                                                                                                             <  6:117117/149‑1 (MQ=255)    aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTgg                                                                                                                                             <  2:151607/149‑1 (MQ=255)    aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTGATTGGTGGGTCATATTTTGCCGTTAAGGTgg                                                                                                                                             >  5:387782/1‑149 (MQ=255)    aaCGAATACCAGATATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTgg                                                                                                                                             <  2:364247/149‑1 (MQ=255)     aCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTGAGTGGTGGGTCAAATGTTGCCTTTAAGGTgtg                                                                                                                                            >  6:310633/1‑147 (MQ=255)        aaTACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAAAGGTGTGTAAAAATTTGACTTAAaggaggctg                                                                                                                                          >  3:160015/1‑145 (MQ=255)         aTACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATTGTTGGGTAAAAAGTTGCATTTAAGGAGGGTCa                                                                                                                                         >  6:329874/1‑148 (MQ=255)          tACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGTGTCaa                                                                                                                                        >  3:202620/1‑148 (MQ=255)            ccAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAg                                                                                                                                     >  7:315258/1‑149 (MQ=255)              aGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGTTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGtt                                                                                                                                   >  5:171104/1‑149 (MQ=255)              aGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGtt                                                                                                                                   <  8:315258/149‑1 (MQ=255)              aGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGAGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTCCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGtt                                                                                                                                   <  4:124145/149‑1 (MQ=255)               gTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATTGGTGGGTAAAAATTTGCCTTTAAGGAGGGTCAAAAttt                                                                                                                                   >  8:222709/1‑148 (MQ=255)                  attattCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGcc                                                                                                                                <  1:111848/148‑1 (MQ=255)                   ttattCAAGCCGTACAACATTAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGGCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGt                                                                                                                              <  3:230403/149‑1 (MQ=255)                      ttCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGGCAAAAGTTGCCGtt                                                                                                                             >  7:146238/1‑147 (MQ=255)                      ttCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGATAGTGGTGGGTAAAAATTTGACTTTTAGGAGGCGCAAAAttttgctatt                                                                                                                            >  2:133047/1‑141 (MQ=255)                           gCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTgg                                                                                                                      <  7:364969/149‑1 (MQ=255)                                 caacaTGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAg                                                                                                                          >  8:265769/1‑139 (MQ=255)                                 caacaTGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAg                                                                                                                          <  7:265769/139‑1 (MQ=255)                                    caTTAAATAACTCAATCAGTCGGGCAATGTTCCCGCCTTTTCTTTGCCTTCATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGTTGGGTCAAAAGTTGCCTTTAAGGTGGGTCAAAAGTTGCCGTTAAg                                                                                                                          <  2:383058/136‑1 (MQ=37)                                    caTGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAg                                                                                                                          >  1:383058/1‑136 (MQ=255)                                      tGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAATTTGCCGTTAAGGGGGCTCAAAATTTGCCGGGTAGGTGGGGGAAAAGTTg                                                                                                           >  7:9976/1‑149 (MQ=255)                                        aaaTAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTAAAAATTTGCCTGTAAGGTGGGTCAAAAGTTGACTATAAGGTGTGTGAAAATTTgac                                                                                                         >  3:225834/1‑147 (MQ=255)                                          aTAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAGAAGTTGCCGa                                                                                                       <  7:278760/149‑1 (MQ=255)                                                             aattatCCCGCCTTTTCTTTGCCTTAATTGCATGAATTCAGGTTGGTAAAAAGTTGCCGTTAGTGTTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTaa                                                                                    <  1:107967/144‑1 (MQ=38)                                                                 ttCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGAGGAGGGTAAAAAGTTGCCGTGAAGGATCGGCAAAAGTTGACGAATACGAGGCTCAAAAGTTGCGGAGGAAAAATTATAAGAGTAAGaa                                                                                 >  2:349343/1‑148 (MQ=16)                                                                   cccGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGGCAAAAGTTGCCCTTAGTGGTGGGTCAAAAGTAGCCGTTAAGGTGGGTAAAAAGTAGCCGTTAAGGTGGGGCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGaa                                                                                 <  5:316140/146‑1 (MQ=255)                                                                         ttttCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAATGGTGGGTAAAAAGTTGCCTTTAAGGTGGGTCAAAATTTGAAGTTAAGGTGTGTCTAAATTTGAATAGTAAGAATTCTACTAATAAGAATTGTACGc                                                                         >  1:317943/1‑148 (MQ=21)                                                                                 tacTTAATTCAATTAATTCATGTGGGTCAAAAGTTGCCTTTATTGGTGGGTAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTgg                                                                                                                      <  6:20015/93‑1 (MQ=18)                                                                                 gCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCACAAGTTGCCTTTAAGGTgg                                                                                                                      >  5:20015/1‑95 (MQ=255)                                                                                  ccTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCAGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGCCGGGAGtt                                                               >  7:62832/1‑149 (MQ=255)                                                                                       aatCCATGAATTCAGGCGGGTCAAAAGACGCCTTTATTGGTGTGTCCAAACTAGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTa                                                          <  1:261659/147‑1 (MQ=37)                                                                                       aTTCAATGAATTCATGTTGGTCAAAAGCTGGCGTTAGTGGGGGGTAAAAACTTGCCTTTAAGGTGGGTCAAAAGTTGCCGTTCAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTa                                                          <  5:310633/149‑1 (MQ=37)                                                                                        tttcATGAATTCTGTTGGCTCAAAAGTACGCTTTAGTGGTGGGTAAAAAGTCGCCTTTACGGTGGGTCAAAAGGTGCCTTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTATGCGACGGGAGTTTTTTa                                                          <  6:190782/145‑1 (MQ=25)                                                                                        ttCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTAAAATTTTGCCGTTAAGGAGGGTCAAAAGTTGAAGTGAAGGGGTGGGAAATTTTGCCGAGTATGGAGTGTACGATTAGGATTTGTTCGCGTCGGGAGtttttttg                                                         >  2:360246/1‑147 (MQ=12)                                                                                                aTTCAGGTTGGTTAAAAGTAGCCTTTATGGGTGGGTCAAAAGTTGCCGTTTAGTTGGGTCAAAAGTTTCCTTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCcgg                                                 <  8:146238/149‑1 (MQ=37)                                                                                                        gggTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAATTTGCCGAGTAAGAATTCTACTAATAAGAATTCTAGGCGACGTGATATTTTTAGCCTCACGGTCGGTCa                                          >  2:180834/1‑148 (MQ=37)                                                                                                                aGTTGCCCTTTCTGGTGGGTAAATAGTTGCCTTTTAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTc                                 <  8:201646/149‑1 (MQ=38)                                                                                                                  ttGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGGCGAGTAAGAATTCTACTATTAAGATTTCTAGGCGACGGGAGTTTTTTATCATCCCTGTCGGTCATAGAGAGTct                                >  5:297106/1‑147 (MQ=37)                                                                                                                   tGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTTCCGAGTAAGATTTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGGCGGTCATAGAGAGTCTcc                              >  5:65457/1‑149 (MQ=255)                                                                                                                           gtggtgGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGTGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGtt                       >  3:313000/1‑148 (MQ=255)                                                                                                                           gtggtgGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGAAAGAATTCTACTATTAAGAATACTAGGCGACGGGAGTATTTTAGACTCCCGCTCGCTCATAGAGAGTCGCCTagagat                       >  4:364381/1‑146 (MQ=37)                                                                                                                           gtggtgGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGGTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGACTTCAAGGCCACGGGCGGTTTTTAGCATCCCGGGCGGTCATAGAGCTTCGCCTAGAGtt                       >  3:216431/1‑148 (MQ=25)                                                                                                                               tggGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCGACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTaaa                    >  2:385526/1‑147 (MQ=255)                                                                                                                                     aaaaGTTGCCTTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGGGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAgaagaa            <  7:222709/149‑1 (MQ=255)                                                                                                                                     aaaaGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAgaagaa            >  2:22158/1‑149 (MQ=255)                                                                                                                                        aGTTGCCGTTAAGGTGGGTAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAatta         <  7:218487/149‑1 (MQ=255)                                                                                                                                         gTTGCCGTTCATGTTGGGCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAattat        <  6:297106/149‑1 (MQ=255)                                                                                                                                          ttGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCGACTATTAAGAATTCTAGGCGACGGGAGGTTTTTTGCCGCCCGGTGGGTCATTGAGAGTCGCCTAGAGTTAAACa                  >  6:367772/1‑138 (MQ=38)                                                                                                                                          gtGCCTTTTAGGTGGGTCAAAAGGTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAattat        <  8:9976/147‑1 (MQ=255)                                                                                                                                               gTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTcgcc  >  7:165498/1‑149 (MQ=255)                                                                                                                                               |                                                                                                                                                     TGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCC  >  NC_000913/2560854‑2561144

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑