Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,563,357	A→G	intergenic (+240/‑235)	yffP → / → yffQ	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	2,563,357	0	A	G	97.8%	163.3 / ‑4.3	46	intergenic (+240/‑235)	yffP/yffQ	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (17/28);  total (17/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

GCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCACAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAA  >  NC_000913/2563210‑2563502                                                                                                                                                    |                                                                                                                                                  gCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGcgca                                                                                                                                                 <  2:475529/150‑1 (MQ=255) gCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGcgca                                                                                                                                                 <  1:604630/150‑1 (MQ=255)   aaaTTTTCCAGATTTCTCGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCGGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTTATGGCCGCCGACGTTGCGCAAtt                                                                                                                                              <  2:597969/151‑1 (MQ=255)         tCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTa                                                                                                                                         <  1:59521/150‑1 (MQ=255)             gATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAAttt                                                                                                                                     >  1:720111/1‑150 (MQ=255)              aTTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCt                                                                                                                                   <  1:291808/151‑1 (MQ=255)              aTTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCt                                                                                                                                   >  2:544198/1‑151 (MQ=255)                         acGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCaaa                                                                                                                        <  1:667036/151‑1 (MQ=255)                          cgcgCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAAt                                                                                                                       <  1:132995/151‑1 (MQ=255)                             gcCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCaa                                                                                                                    <  2:616419/151‑1 (MQ=255)                                aaaaaTAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTc                                                                                                                 >  1:346134/1‑151 (MQ=255)                                   aaTAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTcc                                                                                                                >  2:682265/1‑149 (MQ=255)                                      aaaGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCccacca                                                                                                           <  1:651517/151‑1 (MQ=255)                                        aGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCaaa                                                                                                         <  1:549733/151‑1 (MQ=255)                                         ggCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCaa                                                                                                          >  1:140325/1‑149 (MQ=255)                                            ccAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGcc                                                                                                      >  1:247095/1‑150 (MQ=255)                                                gCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCcaaca                                                                                                  >  2:539584/1‑150 (MQ=255)                                                   gTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGAt                                                                                              <  2:606723/151‑1 (MQ=255)                                                   gTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGAt                                                                                              <  1:288197/151‑1 (MQ=255)                                                     tAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATgg                                                                                            >  1:225510/1‑151 (MQ=255)                                                     tAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATgg                                                                                            >  1:506524/1‑151 (MQ=255)                                                      aGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATggg                                                                                           <  2:611153/151‑1 (MQ=255)                                                         aaCCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAgg                                                                                        >  1:611089/1‑151 (MQ=255)                                                                ccGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAAttt                                                                                 <  2:393875/151‑1 (MQ=255)                                                                ccGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAAttt                                                                                 <  1:453782/151‑1 (MQ=255)                                                                    gCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTtgtg                                                                             <  2:402400/151‑1 (MQ=255)                                                                            cacaATCCCCGCTGACAGTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGa                                                                      <  1:58452/150‑1 (MQ=255)                                                                              caATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATc                                                                    <  2:153869/150‑1 (MQ=255)                                                                               aaTCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGc                                                                  <  2:290000/151‑1 (MQ=255)                                                                                 tCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCtt                                                                >  2:108208/1‑151 (MQ=255)                                                                                            aTTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCa                                                      <  2:503038/150‑1 (MQ=255)                                                                                               atatCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCa                                                  <  1:756902/151‑1 (MQ=255)                                                                                                tatCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCAt                                                 >  1:632355/1‑151 (MQ=255)                                                                                                    aCCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCAttttt                                             >  2:539208/1‑151 (MQ=255)                                                                                                     cccATCTTTCCGGTTTCAGGTGGGGGACTGATTGCCGCCGGCGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGAAGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCAttt                                               <  1:9766/148‑1 (MQ=255)                                                                                                      ccATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGt                                           <  1:656558/151‑1 (MQ=255)                                                                                                            ttCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTaa                                       <  1:388175/149‑1 (MQ=255)                                                                                                                  tttCAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATtcaatc                                <  2:218805/150‑1 (MQ=255)                                                                                                                  tttCAGGTGGGAGACTGATGGCCGACGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATtcaatc                                >  2:580396/1‑150 (MQ=255)                                                                                                                     cAGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACg                            >  2:105586/1‑151 (MQ=255)                                                                                                                      aGGTGGGAGACTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGa                           <  1:709990/151‑1 (MQ=255)                                                                                                                            gagaCTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCa                     <  1:661783/151‑1 (MQ=255)                                                                                                                              gaCTGATGGCCGCCGACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGt                   >  2:702627/1‑151 (MQ=255)                                                                                                                                      gccgccGACGTTGCACAATCTATTAATATCTAATCATTCAAATCAACTCCCACCAAAGCCAACAAGATGGTAGGTGAAGTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCcaa             <  2:388447/149‑1 (MQ=255)                                                                                                                                         gccgACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCcaacaac         >  2:166406/1‑150 (MQ=255)                                                                                                                                          ccgACGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCcaacaacaa       <  1:314819/151‑1 (MQ=255)                                                                                                                                              cGTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATa   <  1:605411/151‑1 (MQ=255)                                                                                                                                               gTTGCGCAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATaa  <  1:67073/151‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                  GCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCACAATTGATTAATTTCTGAACATTCAAATCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAA  >  NC_000913/2563210‑2563502

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑