Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,206,210	T→C	pseudogene (80/792 nt)	jayE →	e14 prophage; putative protein JayE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,206,210	0	T	C	100.0%	198.0 / NA	55	pseudogene (80/792 nt)	jayE	e14 prophage; putative protein JayE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (27/28);  total (27/28)

ACAAAGTGAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGCATTAATCCTGGTCACGCCGGTGAATGGTCTG  >  NC_000913/1206077‑1206346                                                                                                                                      |                                                                                                                                         aCAAAGTGAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTa                                                                                                                                    <  2:1009090/140‑1 (MQ=255)       tGAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGAc                                                                                                                              <  1:38228/140‑1 (MQ=255)                 tGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGAt                                                                                                                    <  2:858021/140‑1 (MQ=255)                                   gctgcCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCggtggt                                                                                                  >  2:93996/1‑140 (MQ=255)                                   gctgcCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCggtggt                                                                                                  >  1:996370/1‑140 (MQ=255)                                   gctgcCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCggtggt                                                                                                  >  1:735083/1‑140 (MQ=255)                                    ctgcCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGgtggtg                                                                                                 >  2:6119/1‑140 (MQ=255)                                     tgcCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGgtgt                                                                                                >  1:260963/1‑140 (MQ=255)                                         cGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTg                                                                                            >  2:888181/1‑140 (MQ=255)                                           tCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTgcg                                                                                          <  2:457920/140‑1 (MQ=255)                                             gATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGcgcg                                                                                        <  1:687008/140‑1 (MQ=255)                                                         gtgGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCt                                                                            >  1:120670/1‑140 (MQ=255)                                                             tataTGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTc                                                                        <  2:120670/140‑1 (MQ=255)                                                             tataTGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTc                                                                        >  1:546289/1‑140 (MQ=255)                                                             tataTGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATCCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTc                                                                        <  2:531380/140‑1 (MQ=255)                                                                  gcgcTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGc                                                                          >  2:1004829/1‑133 (MQ=255)                                                                  gcgcTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGc                                                                          <  1:1004829/133‑1 (MQ=255)                                                                  gcgcTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTg                                                                   >  1:612122/1‑140 (MQ=255)                                                                  gcgcTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTg                                                                   >  1:658837/1‑140 (MQ=255)                                                                  gcgcTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTg                                                                   <  2:546289/140‑1 (MQ=255)                                                                    gcTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCa                                                                 >  2:817189/1‑140 (MQ=255)                                                                     cTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAg                                                                >  1:151324/1‑140 (MQ=255)                                                                      tGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAgg                                                               >  1:927723/1‑140 (MQ=255)                                                                       gggAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGt                                                              >  2:264774/1‑140 (MQ=255)                                                                       gggAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGt                                                              >  2:1086366/1‑140 (MQ=255)                                                                       gggAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGt                                                              <  1:92145/140‑1 (MQ=255)                                                                        ggAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTg                                                             <  1:869013/140‑1 (MQ=255)                                                                        ggAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTg                                                             <  1:817189/140‑1 (MQ=255)                                                                        ggAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTg                                                             >  2:134729/1‑140 (MQ=255)                                                                        ggAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTg                                                             <  1:264774/140‑1 (MQ=255)                                                                          aaGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGcg                                                           >  2:1065657/1‑140 (MQ=255)                                                                               gtCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGcggtcgg                                                      >  1:189848/1‑140 (MQ=255)                                                                                 cAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTa                                                    <  2:658837/140‑1 (MQ=255)                                                                                 cAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTa                                                    <  2:612122/140‑1 (MQ=255)                                                                                  aGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTaa                                                   >  1:999167/1‑140 (MQ=255)                                                                                       tGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTg                                              >  1:938655/1‑140 (MQ=255)                                                                                       tGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTg                                              >  1:214019/1‑140 (MQ=255)                                                                                        ggCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTga                                             <  2:938655/140‑1 (MQ=255)                                                                                            tGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTgacgac                                         <  2:927723/140‑1 (MQ=255)                                                                                                ggTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTa                                     <  1:888181/140‑1 (MQ=255)                                                                                                ggTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTa                                     <  1:134729/140‑1 (MQ=255)                                                                                                ggTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTa                                     <  1:1086366/140‑1 (MQ=255)                                                                                                   gACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACgg                                  >  2:638082/1‑140 (MQ=255)                                                                                                    aCCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGc                                 >  2:144316/1‑140 (MQ=255)                                                                                                    aCCGCCGGGAGTGTTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGc                                 >  2:910350/1‑140 (MQ=255)                                                                                                                gtTATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGCATTAATCCTGGt                     <  2:151324/140‑1 (MQ=255)                                                                                                                  tATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGCATTAATCCTGGTCa                   <  1:6119/140‑1 (MQ=255)                                                                                                                  tATTCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGCATTAATCCTGGTCa                   <  2:735083/140‑1 (MQ=255)                                                                                                                    ttCAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGCATTAATCCTGGTCACg                 <  1:93996/140‑1 (MQ=255)                                                                                                                      cAGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGCATTAATCCTGGTCACGcc               <  2:407743/140‑1 (MQ=255)                                                                                                                       aGCGCGATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGCATTAATCCTGGTCACGCCg              >  1:1042742/1‑140 (MQ=255)                                                                                                                         cgcgATGACCTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGCATTAATCCTGGTCACGCCGGt            >  2:341652/1‑140 (MQ=255)                                                                                                                                 ccTGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGCATTAATCCTGGTCACGCCGGTGAATGGTc    <  1:147057/140‑1 (MQ=255)                                                                                                                                   tGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGCATTAATCCTGGTCACGCCGGTGAATGGTCTg  <  1:1065657/140‑1 (MQ=255)                                                                                                                                   tGGCGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGCATTAATCCTGGTCACGCCGGTGAATGGTCTg  <  2:260963/140‑1 (MQ=255)                                                                                                                                      |                                                                                                                                         ACAAAGTGAAAGCATTTGGCGAAGTGGCTGAACTGCTGCCCGTCGATCCCGGCTGTGTGGTATATGCGCTGGGAAGGTGTCAGCGATGGCCTGAAGGTGACCGCCGGGAGTGTTATTCAGCGCGATGACCTGGTGCAGTACACGACAACTGACGATGCAACCAGCTCCGGTGGTGTCCTGCGCGTGCCGATCGCCTGCTCAAGTGCAGGTGCGGTCGGTAACGCTGACGACGGTACGGCATTAATCCTGGTCACGCCGGTGAATGGTCTG  >  NC_000913/1206077‑1206346

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑