Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006881	3,725,239	2 bp→AA	intergenic (‑71/‑457)	U712_19205 ← / → U712_19210	Uncharacterized protein ywcI/Minor extracellular protease vpr

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	3,725,239	0	G	A	98.1%	164.0 / NA	52	intergenic (‑71/‑458)	U712_19205/U712_19210	Uncharacterized protein ywcI/Minor extracellular protease vpr
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (42/9);  minor base C (1/0);  total (43/9)
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
*	CP006881	3,725,240	0	G	A	100.0%	171.1 / NA	52	intergenic (‑72/‑457)	U712_19205/U712_19210	Uncharacterized protein ywcI/Minor extracellular protease vpr
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (43/9);  total (43/9)

GCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑C‑TT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGTTTTTAGAAGTTT  >  CP006881/3725108‑3725369                                                                                                                                          ||                                                                                                                                  gCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGGC‑T‑TT‑TTA‑GCA‑GCCCGTTTTATCAGCCGCAGCCCGCAAGaaaa                                                                                                                              >  5:352306/1‑139 (MQ=255)       cccAGTTCACCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGACGCAGCCCGCAAGAAAAGACgcc                                                                                                                        >  3:123241/1‑137 (MQ=255)            ttCATCTAAAAGACCATCCACCCCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGGCTGTTTTGCAGGCA‑GC‑CGTT‑TTA‑TCA‑GCCCCTTTTCTCAGCCGCAGCCCGCAAGCACAGACGGCAGagt                                                                                                                   >  5:490599/1‑137 (MQ=255)                      aGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCg                                                                                                         >  4:26887/1‑139 (MQ=255)                        aCCATCCACACCCTAAAAGATACAACCAAACGTTTCATACAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAACAAAAGACGGCCGATTTCTTTTCTCGCa                                                                                                       <  7:145964/139‑1 (MQ=255)                           aTCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCCAGCAAAGACGGCCGAGTTCTTTTGTCGCAAAc                                                                                                    >  2:192137/1‑139 (MQ=255)                            tCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAAc                                                                                                    >  3:349710/1‑138 (MQ=255)                                      tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGctc                                                                                           >  3:200315/1‑137 (MQ=255)                                      tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCGGGCG‑GC‑C‑TTGTTT‑GCA‑GCCCGGTTTCTCAGCCGCAGCCCGCAAGCAAAGCCGGCCGAGGTGTTTTGTCGCCTACTAggggggc                                                                                           >  6:509578/1‑134 (MQ=255)                                      tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGGCC‑GC‑CTTT‑TTA‑GCC‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTGTTTTATCGCAAACTAGCGGctctt                                                                                         >  8:303161/1‑138 (MQ=255)                                      tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGGCA‑GC‑CGGT‑TTA‑GCA‑GCCCGGTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGCTTTCTTTTCTCGCAAACTAGCGGctc                                                                                           >  7:499840/1‑137 (MQ=255)                                         aGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCCGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa                                                                                      <  7:424242/139‑1 (MQ=255)                                          gATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCGAGCa                                                                                      >  1:206543/1‑138 (MQ=255)                                           aTACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCaa                                                                                     >  3:201986/1‑138 (MQ=255)                                           aTACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTGCTTTTTGGCCGGCA‑GC‑CGTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTGCTTTTCTCGGAAACTAGCGGCGCGAGcga                                                                                     >  4:212046/1‑136 (MQ=255)                                             aCAAGCAAACGTTTCATAGATAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGAGGGCCGATTTCTTGTGTCGCAAGCGAGCGGCTCTAGCAAAAc                                                                                  >  8:387818/1‑139 (MQ=255)                                             aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCCGGCG‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGGTCTGTTGTCGCAAACAAGCGGCGCGAGcccaa                                                                                   >  2:184380/1‑134 (MQ=255)                                             aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTGTTTTCTCGCAAACTAGCGGCTCGAGCaaaa                                                                                   >  3:422769/1‑138 (MQ=255)                                             aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCaaaa                                                                                   >  6:390499/1‑138 (MQ=255)                                               aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGATTTCTTTTGTAGCAAACAAGCGGCGCTAGCAAAACt                                                                                 >  5:421838/1‑138 (MQ=255)                                               aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACt                                                                                 >  8:242052/1‑138 (MQ=255)                                               aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCGAGCAAAACt                                                                                 >  7:128358/1‑138 (MQ=255)                                               aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAATTGTTTTCACACAAAATAGCGGCGCAAGCAAAACt                                                                                 >  7:196187/1‑138 (MQ=255)                                               aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCGTTTTTGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCCGCCGCAGCCCCCAAGAAAAGACGGCCGATTTAGTTTCTCGCACAAGAGCGGCACTAGCAAAACt                                                                                 >  6:4979/1‑138 (MQ=255)                                                   aaaCGTTAAATCCAAAAACACCCCCCCGTTTATTTTTGCCAGGCA‑GC‑C‑TT‑TTT‑ACACCCCCGTTTTCTCCGCCCCCGCCCGCAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGa                                                                            <  1:105878/139‑1 (MQ=255)                                                     agttttCATAGAAAAAATTCCCTCGGCTTATTTTTGGCAGGCA‑GC‑A‑TT‑TTACGCA‑GCCCGTTTTCTCCGCGGCAGCCCGAAATAAATCACGGCCTATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                          <  8:128358/136‑1 (MQ=255)                                                     aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAATACGGCCGATTTCTTTTATCGCAAAATAGCGGCTCTAGCAAAACTCATGAct                                                                          >  4:76016/1‑139 (MQ=255)                                                     aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTATTTTATCCCAAACTAGCGGCTCTAGCAAAACTCCAGAct                                                                          >  4:234163/1‑139 (MQ=255)                                                     aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCAGCAGCACGCAAGAAAAGACGGCAGATTACTTTTCTCGCAAACTATCGGCTCAAGCAAAACACATGAc                                                                           >  3:501468/1‑138 (MQ=255)                                                     aCGTTTCATAGAAAAACATCCCTCCGCTTCGTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCCCAAACTAGCGGCTCTAGCAAAACAAATGAc                                                                           >  3:64783/1‑138 (MQ=255)                                                      cGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                          >  6:243099/1‑138 (MQ=255)                                                                aaaaaCATCCCTCCGTTTTTTTTTGGCTGGCC‑GCTT‑TT‑TTC‑GCC‑GCCGGTTTTCTCCGCCGCCGCCCCAAATAAAACACGGCCGATTTCTTTTCTCGAAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGAc                                                               <  4:201986/139‑1 (MQ=255)                                                                          cTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGaaa                                                       >  4:79697/1‑137 (MQ=255)                                                                          cTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGaaa                                                       >  3:424544/1‑137 (MQ=255)                                                                             cGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGaa                                                  >  6:199373/1‑139 (MQ=255)                                                                             cGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTATAGCAAAAAATCGGGTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGaa                                                  >  4:312448/1‑139 (MQ=255)                                                                                  cttTTTGGCCGCCA‑CC‑CTTT‑TTA‑CCC‑GCCCTTTTTCTCCGCCGCCGCCCCAAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCt                                              <  4:185280/138‑1 (MQ=255)                                                                                        ggcaggca‑GC‑CTTT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTca                                        <  5:199373/138‑1 (MQ=255)                                                                                              ca‑gC‑CTTT‑TTA‑GCA‑GCCCGTTTACACAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATg                                 <  1:11347/139‑1 (MQ=255)                                                                                                       t‑ttA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGaa                           >  6:424146/1‑138 (MQ=255)                                                                                                               a‑gcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACGCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAAcc                     >  2:276396/1‑138 (MQ=255)                                                                                                                 gcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAACCTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGACAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCa                    >  5:1007/1‑138 (MQ=255)                                                                                                                 gcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCaa                   >  2:132339/1‑139 (MQ=255)                                                                                                                  cccGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTGTTTTATCGCTAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACGGTGGAAAGCGTATTCTGTGTGCGACTATGTGTGAATAATCCaa                   >  2:167821/1‑138 (MQ=255)                                                                                                                  cccGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCaa                   >  3:433439/1‑138 (MQ=255)                                                                                                                  cccGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAAc                  >  7:151132/1‑139 (MQ=255)                                                                                                                  cccGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAAc                  >  5:240616/1‑139 (MQ=255)                                                                                                                  cccGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTAAGATAGACCGTGGAAAGAGAATTCTTTTTCACAATATGATTTAAAAAACCaa                   >  2:117523/1‑138 (MQ=255)                                                                                                                    cGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTa                <  5:243099/139‑1 (MQ=255)                                                                                                                       tttCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGTCCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGtt             >  6:5881/1‑139 (MQ=255)                                                                                                                        ttCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCGCGAGCAAAACTCATGACTCTATGATAGACCGGGGAAAGAGGATTCTTTGTGTCAATATGATGTAAAAAACCAACGAGttt            >  1:454685/1‑139 (MQ=255)                                                                                                                                  cAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCGTTGTGACAATATGAGTGAAAAAACCCACTAGTTTTTAGAAGttt  >  7:224797/1‑139 (MQ=255)                                                                                                                                          ||                                                                                                                                  GCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑C‑TT‑TTA‑GCA‑GCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGTTTTTAGAAGTTT  >  CP006881/3725108‑3725369

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑