Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	264,750	Δ1 bp	18.7%	intergenic (‑79/+250)	ykfA ← / ← perR	CP4‑6 prophage; putative GTP‑binding protein/CP4‑6 prophage; putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	264,750	0	T	.	18.7%	94.8 / 16.2	32	intergenic (‑79/+250)	ykfA/perR	CP4‑6 prophage; putative GTP‑binding protein/CP4‑6 prophage; putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (13/13);  new base . (3/3);  total (16/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.97e-01

CGGCAAACAGGGCATTGCACAGACTGCTCTTCCCAACACCGGTTTTACCCATAATGCCGATCACTGGCTCGTAGTTAGTTAACTGGTTAATTTGCTGCAGAAGCCGCTCTGATACCCATTGCGGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCCGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTAATGTGAACATGATCAACGAATTTTACCCAGATT  >  CP009273/264497‑265020                                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                                               cGGCAAACAGTGCATTGCACAGCCTGCTCTTCCCAACAACGGTTTTACCCATAATGCCGATCACTGGCTCGTAGTTAGTCAACTGGTTAATTTGCTGCAGAAGCCGCTCTGATACCCATTGCTGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCa                                                                                                                                                                                                                                                           <  1:677473/275‑1 (MQ=255)                                     cacCGGTTTTACCCATAATGCCGATCACTGGCTCGTAGTTAGTTAACTGGTTAATTTGCTGCAGAAGCCGCTCTGATACCCATTGCGGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGACGTTAATTGCGTATGTTCAGAGTGATGATATATAATTGAAGATTTTTTCAATACTCTGCGCTTGAGGCAGCTTAGCGActgttttg                                                                                                                                                                                                                       >  2:605404/1‑270 (MQ=255)                                     cacCGGTTTTACCCATAATGCCGATCACTGGCTCGTAGTTAGTTAACTGGTTAATTTGCTGCAGAAGCAGCTCTGATACCCATGGCGGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTAAGAGTAATGATATATATATGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTACCCGCCTGATGGc                                                                                                                                                                                                                       >  2:48897/1‑275 (MQ=255)                                          gTTTTACCCATAATGCCGATCACTGGCTCGTCGTTAGTTAACTGGTTAATTTGCTGCACAAGCCGCTCTGATACCCATTGCGGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGATTGAGGCAGCTGCGAGACTGCTAGCTCAgg                                                                                                                                                                                                                  >  1:245727/1‑275 (MQ=255)                                                            aTCACTGGCTCGTAGTTAGTTAACTGGTTAATTTGCTGCAGAAGCCGCTCTGATACCCATTGCGGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCTGCCGTTAATTGCGTATGTTCAGAGTGATGatatata                                                                                                                                                                                                                                                                           >  1:72466/1‑200 (MQ=255)                                                                cTGGCTCGTAGTTAGTTAACTGGTTAATTTGCTGCAGAAGCCGCTCTGATACCCATTGCGGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTg                                                                                                                                                                                                                                                                       <  2:72465/200‑1 (MQ=255)                                                                 tGGCTCGTAGTTAGTTAACTTGTTAATTTGCTGCAGAAGCCGCTCTGATACCCATTGCGGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATagcag                                                                                                                                                                                           <  1:173201/275‑1 (MQ=255)                                                                             agttaACTGGTTAATTTGCTGCAGAAGCCGCTCTGATACCCATTGCGGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACa                                                                                                                                                                               <  1:256819/275‑1 (MQ=255)                                                                               ttaACTGGTTAATTTGCTGCAGAAGCCGCTCTGATACCCATTGCGGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTgcgc                                                                                                                                                                                                                                                >  2:239501/1‑208 (MQ=255)                                                                                   cTGGTTAATTTGCTGCAGAAGCCGCTCTGATACCCATTGCGGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGa                                                                                                                                                                                                                                            <  1:239506/208‑1 (MQ=255)                                                                                          aTTTGCTGCAGAAGCCGCTCTGATACCCATTGCGGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTANAATCGTGAGATTACGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTAtt                                                                                                                                                                     <  1:605413/272‑1 (MQ=255)                                                                                                              tGATACCCATTGCGGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCCGCCGTGATa                                                                                                                                               <  1:48897/274‑1 (MQ=255)                                                                                                                                                                               tcaCTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGatat                                                                                                                                                                                                                                                                              <  2:259930/82‑1 (MQ=255)                                                                                                                                                                                caCTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGAtttttt                                                                                                                                                                                                                                                             >  2:596033/1‑98 (MQ=255)                                                                                                                                                                                caCTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCtt                                                                                                                                                                                                                                              >  1:115157/1‑113 (MQ=255)                                                                                                                                                                                caCTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCaa                                                                                                                                                                                                               >  2:209665/1‑144 (MQ=255)                                                                                                                                                                                    actCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAAt                                                                                                                                                                                                                                                         <  1:596042/98‑1 (MQ=255)                                                                                                                                                                                    actCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGatg                                                                                                                                                                                                                                          <  2:115156/113‑3 (MQ=255)                                                                                                                                                                                    actCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCaatgaa                                                                                                                                                                                                           <  1:209669/144‑1 (MQ=255)                                                                                                                                                                                     ctcctcTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCa                                                                                                                                                                                                                >  2:665540/1‑138 (MQ=255)                                                                                                                                                                                     ctcctcTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCCGCCGTGATACACCTTAAAATCTAAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAATGAGAGCATTCAAAAaataatac                                                                         >  2:642499/1‑271 (MQ=255)                                                                                                                                                                                        ctctGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGActgct                                                                                                                                                                                                                          >  2:552768/1‑125 (MQ=255)                                                                                                                                                                                         tctGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCaatga                                                                                                                                                                                                            <  1:665549/138‑1 (MQ=255)                                                                                                                                                                                            gAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCt                                                                                                                                                                                                                      <  1:552777/125‑1 (MQ=255)                                                                                                                                                                                                    ataaAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGatatata                                                                                                                                                                                                                                                                           >  2:412580/1‑64 (MQ=255)                                                                                                                                                                                                       aaaaaCGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGA‑ATAATTCTGAAg                                                                                                                                                                                                                                                                    >  1:295879/1‑67 (MQ=255)                                                                                                                                                                                                       aaaaaCGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGA‑ATAATTCTGAAg                                                                                                                                                                                                                                                                    >  1:475100/1‑67 (MQ=255)                                                                                                                                                                                                       aaaaaCGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGA‑ATAATTCTGAAg                                                                                                                                                                                                                                                                    >  2:516364/1‑67 (MQ=255)                                                                                                                                                                                                        aaaaCGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTg                                                                                                                                                                                                                                                                       <  1:412587/64‑1 (MQ=255)                                                                                                                                                                                                           aCGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGA‑ATAATTCTGAAGGttt                                                                                                                                                                                                                                                                <  2:475093/67‑1 (MQ=37)                                                                                                                                                                                                           aCGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGA‑ATAATTCTGAAGGttt                                                                                                                                                                                                                                                                <  2:295873/67‑1 (MQ=37)                                                                                                                                                                                                           aCGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGATCAGAGTGATGA‑ATAATTCTGAAGGttt                                                                                                                                                                                                                                                                <  1:516371/67‑1 (MQ=25)                                                                                                                                                                                                                       tGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATAGAGAGGATGAGCCGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTAAGTAATAAAGTTACTTTGAATTCAGAGccacaat                                     >  1:642986/1‑270 (MQ=255)                                                                                                                                                                                                                                             tATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCCGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAAAGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTAATGTGAACATGAACaaataa               >  2:508455/1‑271 (MQ=255)                                                                                                                                                                                                                                                     gagTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCt                                                                                                                                                                                                                                     >  1:703721/1‑53 (MQ=255)                                                                                                                                                                                                                                                         gatgatATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTgcgc                                                                                                                                                                                                                                 <  2:703711/53‑1 (MQ=255)                                                                                                                                                                                                                                                          atgttATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGNATTTACTAACAGGGATTTATTGAGAGTATGAGCCGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTAATGTGAACTTGATCAATGAATTTTACCCAGAt   <  1:508462/274‑1 (MQ=255)                                                                                                                                                                                                                                                          atgatATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCGGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCCGCCGTGATACACCTTAAAATCTCAACCGAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAGAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTAATGTGAACATGATCAACGAATTTTACCCAGAtt  >  1:685793/1‑275 (MQ=255)                                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                                               CGGCAAACAGGGCATTGCACAGACTGCTCTTCCCAACACCGGTTTTACCCATAATGCCGATCACTGGCTCGTAGTTAGTTAACTGGTTAATTTGCTGCAGAAGCCGCTCTGATACCCATTGCGGCAGATCAGCAAGCGATTGCTGAAACGACTTCAAACCTTCAGAATTATTCATCACTACTCCTCTGAAAAATAATAAAAAACGGTAGAATCGTGAGATTCCGCCGTTAATTGCGTATGTTCAGAGTGATGATATATATCTGAAGATTTTTTCAATCCTCTGCGCTTGAGGCAGCTGCGCGACTGCTGGCTCAGGCAATGAATGAGTTATAATAGCAGCATTTACTAACAGGGATTTATTGAGAGTATGAGCCGCCGTGATACACCTTAAAATCTCAACCCAGCAAAGTTTCGGAGCCGCGAGCAAAAGTGAGAGCCTTCACAAAATAATGCTTAGTAATAAAGTTACTTTGAATTCAGAGCCCCGATTAATGTGAACATGATCAACGAATTTTACCCAGATT  >  CP009273/264497‑265020

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑