Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,500,253	(C)5→6	pseudogene (539/1199 nt)	yjgX ←	KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,500,248	1	.	C	100.0%	176.3 / NA	50	pseudogene (544/1199 nt)	yjgX	KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (31/19);  total (31/19)

GGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCT‑CCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAGTCATAAATCAGTGTCCGGCTCAGGGAAGAC  >  NC_000913/4500112‑4500376                                                                                                                                          |                                                                                                                                 ggATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCT‑ccc                                                                                                                               <  2:243810/140‑1 (MQ=255)          cGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGtttt                                                                                                                       >  2:147767/1‑140 (MQ=255)           gCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTc                                                                                                                      <  1:147767/140‑1 (MQ=255)            ccAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTcc                                                                                                                     <  1:581690/140‑1 (MQ=255)            ccAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTcc                                                                                                                     >  2:591754/1‑140 (MQ=255)               gcgcACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTg                                                                                                                  <  1:332365/140‑1 (MQ=255)                cgcACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGa                                                                                                                 >  1:726531/1‑140 (MQ=255)                cgcACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGa                                                                                                                 >  1:30904/1‑140 (MQ=255)                 gcACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGAt                                                                                                                <  2:71676/140‑1 (MQ=255)                 gcACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGAt                                                                                                                <  1:494038/140‑1 (MQ=255)                    cGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTgg                                                                                                             <  2:30904/140‑1 (MQ=255)                          gTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATcc                                                                                                       >  1:427465/1‑140 (MQ=255)                          gTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATcc                                                                                                       >  1:260691/1‑140 (MQ=255)                             tCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATccacc                                                                                                    <  2:260691/140‑1 (MQ=255)                              ccTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATcc                                                                                                       <  1:49521/136‑1 (MQ=255)                              ccTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATcc                                                                                                       >  2:49521/1‑136 (MQ=255)                                tGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCAtg                                                                                                 >  1:517091/1‑140 (MQ=255)                                tGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCAtg                                                                                                 >  2:299164/1‑140 (MQ=255)                                     caacaGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTg                                                                                            >  1:474447/1‑140 (MQ=255)                                             tGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGc                                                                                    >  2:527045/1‑140 (MQ=255)                                                 aTCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCtttt                                                                                >  1:46817/1‑140 (MQ=255)                                                   cTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTtgc                                                                              >  1:474209/1‑140 (MQ=255)                                                         tACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAg                                                                        <  2:318085/140‑1 (MQ=255)                                                              gaagcgaagcTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGcca                                                                   >  1:134746/1‑140 (MQ=255)                                                                agcgaagcTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGccacc                                                                 >  1:105759/1‑140 (MQ=255)                                                                agcgaagcTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGccacc                                                                 >  1:281923/1‑140 (MQ=255)                                                                agcgaagcTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGccacc                                                                 >  2:361943/1‑140 (MQ=255)                                                                        tGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACAttgtt                                                         >  2:124636/1‑140 (MQ=255)                                                                            tttCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCg                                                     >  2:465387/1‑140 (MQ=255)                                                                            tttCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCg                                                     >  2:713174/1‑140 (MQ=255)                                                                                  gAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCa                                               <  2:427465/140‑1 (MQ=255)                                                                                       aaGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGtt                                          <  2:474447/140‑1 (MQ=255)                                                                                       aaGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGtt                                          <  2:17857/140‑1 (MQ=255)                                                                                       aaGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGtt                                          <  1:713174/140‑1 (MQ=255)                                                                                          tGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGt                                           >  2:248032/1‑136 (MQ=255)                                                                                          tGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGt                                           <  1:248032/136‑1 (MQ=255)                                                                                          tGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTg                                       >  2:696635/1‑140 (MQ=255)                                                                                               tGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCAt                                  <  2:281923/140‑1 (MQ=255)                                                                                               tGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCAt                                  <  1:465387/140‑1 (MQ=255)                                                                                                 cTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAg                                >  2:356470/1‑140 (MQ=255)                                                                                                    cGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAGTCa                             >  1:200322/1‑140 (MQ=255)                                                                                                    cGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAGTCa                             >  2:647001/1‑140 (MQ=255)                                                                                                            aaGCAATAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAGTCATAAATCAg                     >  1:639003/1‑140 (MQ=255)                                                                                                                aaTAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAGTCATAAATCAGTGTc                 <  1:591754/140‑1 (MQ=255)                                                                                                                 aTAACAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAGTCATAAATCAGTGTcc                <  2:639003/140‑1 (MQ=255)                                                                                                                    aCAGAGATGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAGTCATAAATCAGTGTCCGGc             <  2:517091/140‑1 (MQ=255)                                                                                                                         gaTGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAGTCATAAATCAGTGTCCGGCTCAgg        >  2:720866/1‑140 (MQ=255)                                                                                                                         gaTGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAGTCATAAATCAGTGTCCGGCTCAgg        >  2:346330/1‑140 (MQ=255)                                                                                                                         gaTGCGTGTGTCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAGTCATAAATCAGTGTCCGGCTCAgg        >  2:465335/1‑140 (MQ=255)                                                                                                                               tgtgtCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAGTCATAAATCAGTGTCCGGCTCAGGGAAGac  >  2:671371/1‑140 (MQ=255)                                                                                                                               tgtgtCATGCTCCCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAGTCATAAATCAGTGTCCGGCTCAGGGAAGac  >  1:525691/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                 GGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGAGGAAAGTGGCATGCTCCGCATCAGAAGCAATAACAGAGATGCGTGTGTCATGCT‑CCCCCAGTTTTCCTTGATTGGATATCCACCATGTGCTGTATCCTGCTTTTGCTGCCAGCGCCACCACATTGTTGCCGGAATCAGGGTTCTGCTCATAGTCATAAATCAGTGTCCGGCTCAGGGAAGAC  >  NC_000913/4500112‑4500376

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: ‑