Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,012,563	(G)6→7	pseudogene (62/279 nt)	intG →	putative defective phage integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,012,557	1	.	G	100.0%	118.8 / NA	34	pseudogene (56/279 nt)	intG	putative defective phage integrase
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base G (12/22);  total (12/22)

CGCTCATATCCATCGCCCGGAATATGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑GGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAA  >  NC_000913/2012426‑2012686                                                                                                                                     |                                                                                                                                  cGCTCATATCCATCGCCCGGAATATGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑gggggggt                                                                                                                           >  2:350756/1‑138 (MQ=255)  gCTCATATCCATCGCCCGGAATATGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑gggggggtt                                                                                                                          <  2:483009/140‑4 (MQ=255)  gCTCATATCCATCGCCCGGAATATGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑gggggggtt                                                                                                                          <  1:284897/140‑4 (MQ=255)   cTCATATCCATCGCCCGGAATATGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑gggggggtta                                                                                                                         >  1:419875/1‑136 (MQ=255)    tCATATCCATCGCCCGGAATATGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑gggggggttat                                                                                                                        <  1:546390/140‑6 (MQ=255)           cATCGCCCGGAATATGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGtat                                                                                                                  <  1:228069/140‑1 (MQ=255)            aTCGCCCGGAATATGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGtata                                                                                                                 <  2:201859/140‑1 (MQ=255)              cGCCCGGAATATGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGtat                                                                                                                  <  2:57772/137‑1 (MQ=255)              cGCCCGGAATATGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGtat                                                                                                                  >  1:57772/1‑137 (MQ=255)                cccGGAATATGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGa                                                                                                             >  2:342798/1‑140 (MQ=255)                cccGGAATATGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGa                                                                                                             <  2:297429/140‑1 (MQ=255)                       tatGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGa                                                                                                      <  2:262778/140‑1 (MQ=255)                        atGAATAAAAACATCAACAAAGAATAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGAt                                                                                                     <  1:301318/140‑1 (MQ=255)                               aaaaCATCAACAAAGATTAAATTATCCAGTGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGaa                                                                                              >  2:454061/1‑140 (MQ=255)                                    aTCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGt                                                                                         <  1:72208/140‑1 (MQ=255)                                     tCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGtt                                                                                        <  1:350756/140‑1 (MQ=255)                                         caaAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAgg                                                                                    <  1:473456/140‑1 (MQ=255)                                           aaGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGAt                                                                                  <  2:419875/140‑1 (MQ=255)                                           aaGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGAt                                                                                  <  1:8018/140‑1 (MQ=255)                                                       tCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCAtt                                                                      >  1:328133/1‑140 (MQ=255)                                                           gagGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTaa                                                                  <  2:69651/140‑1 (MQ=255)                                                                 aCTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGa                                                            >  1:204972/1‑140 (MQ=255)                                                                        cGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATtgag                                                     <  1:237751/140‑1 (MQ=255)                                                                          tCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATtgagtg                                                   >  2:58754/1‑140 (MQ=255)                                                                          tCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATtgagtg                                                   >  2:514839/1‑140 (MQ=255)                                                                                gTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGttta                                             <  1:454061/140‑2 (MQ=255)                                                                                  cGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGcc                                           <  2:290057/140‑1 (MQ=255)                                                                                   gTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGccc                                          <  2:204972/140‑1 (MQ=255)                                                                                    tAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGcccc                                         >  2:438156/1‑140 (MQ=255)                                                                                    tAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGc                                            >  2:315437/1‑137 (MQ=255)                                                                                    tAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGc                                            <  1:315437/137‑1 (MQ=255)                                                                                                  gtggtgATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCAcg                           >  2:52673/1‑140 (MQ=255)                                                                                                   tggtgATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCAcgc                          >  1:264296/1‑140 (MQ=255)                                                                                                      tgATGTGTCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGt                       <  1:514839/140‑1 (MQ=255)                                                                                                          gtgtCAAATGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTgaga                   <  1:52673/140‑1 (MQ=255)                                                                                                                 aTGAGACGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATg            <  1:157510/140‑1 (MQ=255)                                                                                                                     gaCGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATg            <  2:148057/136‑1 (MQ=255)                                                                                                                     gaCGCTCTGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATg            >  1:148057/1‑136 (MQ=255)                                                                                                                           ctGATGTTCAGGGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTaacaa  <  2:98501/140‑1 (MQ=255)                                                                                                                                     |                                                                                                                                  CGCTCATATCCATCGCCCGGAATATGAATAAAAACATCAACAAAGATTAAATTATCCAGAGGTTACTGTTGCGTCTGTGGTCGTAACAACATCCGACGTGGTGATGTGTCAAATGAGACGCTCTGATGTTCA‑GGGGGGTTATCGCGTATACGGATCGTGGATGGCAGAAAACGTTCAGGATCAGGTATCCATTTTAAACCAGAAATTGAGTGAGTTTGCCCCATCCATGCCCCACGCGGTGAGATCGGATGTAATTAACAA  >  NC_000913/2012426‑2012686

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: ‑