Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,510,046	A→G	pseudogene (243/330 nt)	yjhV →	KpLE2 phage‑like element; putative uncharacterized protein YjhV

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,510,046	0	A	G	100.0%	192.2 / NA	55	pseudogene (243/330 nt)	yjhV	KpLE2 phage‑like element; putative uncharacterized protein YjhV
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (20/35);  total (20/35)

CGGCTCTATCGCTGAATCATGGCGTCAGCAGCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCACTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCGGTGATTAAGAAAGCTGCACCTACCTAAGTAGTAGCAA  >  NC_000913/4509917‑4510181                                                                                                                                  |                                                                                                                                        cGGCTCTATCGCTGAATCATGGCGTCAGCAGCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCAT‑‑‑‑‑‑‑GCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCgg                                                                                                                        <  1:337487/140‑1 (MQ=255)  ggCTCTATCGCTGAATCATGGCGTCAGCAGCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAg                                                                                                                              <  1:449261/140‑1 (MQ=255)      ctATCGCTGAATCATGGCGTCAGCAGCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTc                                                                                                                          <  1:158899/140‑1 (MQ=255)        gtCGCTGAATCATGGGGTCAGCAGCAGTGGACACCATACTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCgg                                                                                                                        <  1:352390/139‑1 (MQ=255)        aTCGCTGAATCATGGCGTCAGCAGCTGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCgg                                                                                                                        <  1:309356/140‑1 (MQ=255)          cGCTGAATCATGGCGTCAGCAGCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTa                                                                                                                      <  1:694345/140‑1 (MQ=255)            cTGAATCATGGCGTCAGCAGCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAg                                                                                                                    <  1:165532/140‑1 (MQ=255)            cTGAATCATGGCGTCAGCAGCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAg                                                                                                                    <  2:46187/140‑1 (MQ=255)            cTGAATCATGGCGTCAGCAGCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGATTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAg                                                                                                                    <  1:476145/140‑1 (MQ=255)              gAATCATGGCGTCAGCAGCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAGGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCt                                                                                                                  <  2:819601/140‑1 (MQ=255)                    tGGCGTCAGCAGCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGAACGGGCCCATCTACTTACGCTTTATTCCAGCTTCGGTAAGCTGGGTgc                                                                                                            >  2:352390/1‑139 (MQ=255)                         tCAGCAGCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGacac                                                                                                       >  2:628699/1‑140 (MQ=255)                          cagcagCCGTGCACACCATCCTCTTGTTGTGACTGTGAGCCTGCCACCGTGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACAcc                                                                                                      <  2:333655/140‑1 (MQ=255)                          cagcagCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACAcc                                                                                                      <  1:555099/140‑1 (MQ=255)                          cagcagCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACAcc                                                                                                      <  1:525892/140‑1 (MQ=255)                           agcagcCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCg                                                                                                     >  1:802318/1‑140 (MQ=255)                            gcagcCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGa                                                                                                    <  1:531852/140‑1 (MQ=255)                            gcagcCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGa                                                                                                    <  1:611243/140‑1 (MQ=255)                              agcCGTGCACACCATCCTATTGCTGTGACCGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACt                                                                                                  <  1:224264/140‑1 (MQ=255)                                 cGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCAt                                                                                               <  2:612592/140‑1 (MQ=255)                                     cacaCCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATACCAGCTTAGGTAAGCTGGGTGAGACACCGACTCATGAAg                                                                                           >  2:275137/1‑140 (MQ=255)                                          cATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATc                                                                                      >  1:679516/1‑140 (MQ=255)                                           aTCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCa                                                                                     <  2:647629/140‑1 (MQ=255)                                                aTTGTTGTGACTGGGAGGCTGCAACTATGCTTCGCGCGTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGAt                                                                                <  1:253594/140‑1 (MQ=255)                                                    ttgtGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACa                                                                            >  1:85608/1‑140 (MQ=255)                                                    ttgtGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACa                                                                            <  2:679516/140‑1 (MQ=255)                                                    ttgtGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACa                                                                            >  2:115161/1‑140 (MQ=255)                                                      gtgACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAAt                                                                          >  2:616240/1‑140 (MQ=255)                                                      gtgACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAAt                                                                          >  2:541154/1‑140 (MQ=255)                                                         aCTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGCGACACCGACTCATGAAGATATCATTGATAACAATCGa                                                                       >  1:363535/1‑140 (MQ=255)                                                         aCTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGCAAGCTGGGAGAGCCACAGACTCATGGAGATATCATTGATAACAATCGa                                                                       >  2:289565/1‑140 (MQ=255)                                                                   tGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACt                                                             <  1:541154/140‑1 (MQ=255)                                                                     ccaccaTGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTgg                                                           <  1:196635/140‑1 (MQ=255)                                                                      caccaTGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGc                                                          <  2:802318/140‑1 (MQ=255)                                                                      caccaTGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGc                                                          <  2:693954/140‑1 (MQ=255)                                                                                cgcgCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCGTGAAGATAGCATAGATCACAATCGAACCATGAACTGGCCTGTATAACg                                                >  2:243994/1‑140 (MQ=255)                                                                                cgcgCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACg                                                >  2:657917/1‑140 (MQ=255)                                                                                     tttCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCt                                           <  2:85169/140‑1 (MQ=255)                                                                                       tCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGc                                                          >  1:755835/1‑123 (MQ=255)                                                                                       tCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGc                                                          <  2:755835/123‑1 (MQ=255)                                                                                       tCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGAAATCATTGACAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGc                                         >  2:271935/1‑140 (MQ=255)                                                                                         ccTCTGGCGAAAAAGTGAGAAGGACTGGCTCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCg                                       <  1:361634/140‑1 (MQ=255)                                                                                         ccTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCg                                       <  1:616240/140‑1 (MQ=255)                                                                                                      aGGGAGAAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCGGTGATTAAGAAAg                          <  1:659980/140‑1 (MQ=255)                                                                                                           gaAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCGGTGATTAAGAAAGCTGCa                     <  2:153489/140‑1 (MQ=255)                                                                                                           gaAGGACGGGCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCGGTGATTAAGAAAGCTGCa                     <  1:116389/140‑1 (MQ=255)                                                                                                             aGGACGGGCCCGTCTGCATTCGATTTATGCCCGTTGCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCGGTGATTAAGAAAGCTGCacc                   <  2:363535/140‑1 (MQ=255)                                                                                                                  gggCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGCCTGCCGGTCATTACGAAAGCTGCacctacct              >  2:357256/1‑140 (MQ=255)                                                                                                                    gCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCGGTGATTAAGAAAGCTGCa                     <  1:734249/131‑1 (MQ=255)                                                                                                                    gCCCGTCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCGGTGATTAAGAAAGCTGCa                     >  2:734249/1‑131 (MQ=255)                                                                                                                         tCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCGGTGATTAAGAAAGCTGCACCTACCTAagtagt       <  2:588448/140‑1 (MQ=255)                                                                                                                         tCTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTAATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCGGTCATTCAGCAAGCTGTACCTACCTAagtagt       >  1:384564/1‑140 (MQ=255)                                                                                                                          cTGCCTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCGGTGATTAAGAAAGCTGCACCTACCTAAgtagta      >  2:664079/1‑140 (MQ=255)                                                                                                                           tGCCTTCGCTTTATGTCAGCTTTGGCAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCGGTGATTAAGAAAGCTGCACCTACCTAAGtagtag     <  1:289565/140‑1 (MQ=255)                                                                                                                              cTTCGCTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCGGTGATTAAGAAAGCTGCACCTACCTAAGTAGTAGCaa  >  2:182122/1‑140 (MQ=255)                                                                                                                                  |                                                                                                                                        CGGCTCTATCGCTGAATCATGGCGTCAGCAGCCGTGCACACCATCCTATTGTTGTGACTGGGAGGCTGCCACCATGCTTCGCGCTTTCCCTCTGGCGAAAAAGGGAGAAGGACGGGCCCGTCTGCCTTCACTTTATGCCAGCTTCGGTAAGCTGGGTGAGACACCGACTCATGAAGATATCATTGATAACAATCGATCCATCAACTGGCCTGTATAACGTGGCTGCCGGTGATTAAGAAAGCTGCACCTACCTAAGTAGTAGCAA  >  NC_000913/4509917‑4510181

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: ‑