Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,206,680	A→G	pseudogene (550/792 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	1,206,680	0	A	G	100.0%	174.5 / NA	50	pseudogene (550/792 nt)	jayE	e14 prophage; putative protein JayE
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (30/20);  total (30/20)

TCGGTGTGATGATTGCCAGCAGTGACCTGATTAATCCCATTCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATACGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGCAGGGAGAACTCAAGGTATCGCGTATCAGTGAG  >  NC_000913/1206543‑1206811                                                                                                                                          |                                                                                                                                    tCGGTGTGATGATTGCCAGCAGTGACCTGATTAATCCCATTCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCg                                                                                                                                   >  1:104476/1‑140 (MQ=255) tCGGTGTGATGATTGCCAGCAGTGACCTGATTAATCCCATTCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCg                                                                                                                                   >  1:27453/1‑140 (MQ=255)     tgtgATGATTGCCAGCAGTGACCTGATTAATCCCATTCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTgg                                                                                                                               <  2:163237/140‑1 (MQ=255)              tGCCAGCAGTGACCTGATTAATCCCATTCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGGGTTCAGGCCGGTGGCACATGCGGTGGATTTTCata                                                                                                                      >  2:361275/1‑140 (MQ=255)               gCCAGCAGTGACCTGATTAATCCCATTCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATCTGTTCAGGCCGATGACACATGCGGTGGATTTTCatat                                                                                                                     >  1:340236/1‑140 (MQ=255)                         aCCTGATTAATCCCATTCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACg                                                                                                           >  1:717897/1‑140 (MQ=255)                         aCCTGATTAATCCCATTCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACg                                                                                                           >  1:62177/1‑140 (MQ=255)                          ccTGATTAATCCCATTCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGc                                                                                                          >  2:135030/1‑140 (MQ=255)                              aTTAATCCCATTCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGGGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGa                                                                                                      >  1:696098/1‑140 (MQ=255)                               ttAATCCCATTCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGac                                                                                                     <  2:27453/140‑1 (MQ=255)                               ttAATCCCATTCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGac                                                                                                     <  2:104476/140‑1 (MQ=255)                                        ttCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGaca                                                                                                    <  1:141239/132‑1 (MQ=255)                                        ttCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGaca                                                                                                    >  2:141239/1‑132 (MQ=255)                                        ttCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGa                                                                                                      <  2:33733/130‑1 (MQ=255)                                        ttCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGa                                                                                                      >  1:33733/1‑130 (MQ=255)                                        ttCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGAGGATTTTCATAGCCACGTGACGCCGGACACACCAGaa                                                                                            >  1:349672/1‑140 (MQ=255)                                             gaagaaTCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACGTGCGGTGGTTTTACATGTCCGCGTGTCGCCCGACACACCAGAAATACg                                                                                       >  2:349170/1‑140 (MQ=255)                                              aagaaTCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACgg                                                                                      <  2:79465/140‑1 (MQ=255)                                              aagaaTAAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACgg                                                                                      <  2:55413/140‑1 (MQ=255)                                                   tCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGc                                                                                 >  1:48132/1‑140 (MQ=255)                                                        ggAAACGGCGGCAAGACAACATCTCGGGCCATTGGACCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTa                                                                            <  2:349672/140‑1 (MQ=255)                                                            aCGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCCTATCCGCGAGACACCGTACACACCAGAAATGCGGGCTGCCATTACcgc                                                                        >  2:252928/1‑140 (MQ=255)                                                                cggcAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAg                                                                    >  1:603592/1‑140 (MQ=255)                                                                  gcAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGtt                                                                  <  2:62177/140‑1 (MQ=255)                                                                  gcAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGtt                                                                  <  2:717897/140‑1 (MQ=255)                                                                           caTATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGACACACGGGCTGCCTTTACCGCGGAGTTGcgttcgtt                                                         >  2:372534/1‑140 (MQ=255)                                                                               tCGGGCCACTGGCCCCGGTGGCCGGTTCTCATTTGTACGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCctg                                                     <  1:252928/140‑1 (MQ=255)                                                                                cGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATGCGGGCTGGCATAACGGCGGAGGTGCGTTCGTTCctgc                                                    >  1:221814/1‑140 (MQ=255)                                                                                  ggCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACCCCAGAAATCCGGACTGACATTACCGGGGAGGTGCGTTCGTTCctgctg                                                  >  2:253315/1‑140 (MQ=255)                                                                                   gCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCtgctgc                                                 >  1:387634/1‑140 (MQ=255)                                                                                    ccACTGGCCCCGGTGGCTGGCTTTGATTTGTTTGTTTTCAGGCCGGTGACACATGCCGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCg                                                <  2:341589/140‑1 (MQ=255)                                                                                     cACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGt                                               >  1:64595/1‑140 (MQ=255)                                                                                     cACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGt                                               >  2:789542/1‑140 (MQ=255)                                                                                      aCTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGTCTGGCATTACCGCGGACTTGCGTTCGTTCCTGCTGCGTg                                              >  2:245141/1‑140 (MQ=255)                                                                                       cTGGCCCCGGTGGCAGGCTCTGGTTTGTATGGGTTTAGGGCGGTGGCAGATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGa                                             <  2:340236/140‑1 (MQ=255)                                                                                       cTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGcgtt                                                             >  2:574206/1‑124 (MQ=255)                                                                                       cTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGcgtt                                                             <  1:574206/124‑1 (MQ=255)                                                                                                  ggCAGGCTCTGATTTTTATGTGGTCGGGCGGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGc                                  <  1:349170/140‑1 (MQ=255)                                                                                                  ggCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGc                                  <  1:789542/140‑1 (MQ=255)                                                                                                  ggCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGc                                  <  2:696098/140‑1 (MQ=255)                                                                                                         tctGATTTGTATGTGGTCAGGCGGGGGGCCCATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGCAGGgaga                           <  1:372534/140‑1 (MQ=255)                                                                                                              tttGTATGTGTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGCAGGGAGAACTCa                      <  2:57552/140‑1 (MQ=255)                                                                                                                    tgtgTTCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGCAGGGAGAACTCAAGGTAt                <  1:135030/140‑1 (MQ=255)                                                                                                                         tCAGGCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCTTGATGGTCATCAGCGGGGAGACCTCAAGGTATCGCGt           >  1:344434/1‑140 (MQ=255)                                                                                                                            ggCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGAGGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGCAGGGAGAACTCAAGGTATCGCGTATc        >  2:30520/1‑140 (MQ=255)                                                                                                                            ggCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGCAGGGAGAACTCAAGGTATCGCGTATc        >  2:572146/1‑140 (MQ=255)                                                                                                                            ggCCGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGCAGGGAGAACTCAAGGTATCGCGTATc        >  1:432623/1‑140 (MQ=255)                                                                                                                               cGGTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGCAGGGAGAACTCAAGGTATCGCGTATCAGt     <  2:387634/140‑1 (MQ=255)                                                                                                                                ggTGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGCAGGGAGAACTCAAGGTATCGCGTATCAGTg    >  2:837197/1‑140 (MQ=255)                                                                                                                                  tGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGCAGGGAGAACTCAAGGTATCGCGTATCAGTGAg  >  2:625245/1‑140 (MQ=255)                                                                                                                                  tGGCACATGCGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGCAGGGAGAACTCAAGGTATCGCGTATCAGTGAg  >  2:776522/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                    TCGGTGTGATGATTGCCAGCAGTGACCTGATTAATCCCATTCCGGAAGAATCAACGGAAACGGCGGCAAGACAACATATCGGGCCACTGGCCCCGGTGGCAGGCTCTGATTTGTATGTGTTCAGGCCGGTGGCACATACGGTGGATTTTCATATCCGCGTGACGCCGGACACACCAGAAATACGGGCTGCCATTACCGCGGAGTTGCGTTCGTTCCTGCTGCGTGATGGTTATCCGCAGGGAGAACTCAAGGTATCGCGTATCAGTGAG  >  NC_000913/1206543‑1206811

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑