Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,467,417	A→G	pseudogene (24/468 nt)	rpsG ←	30S ribosomal protein S7

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,467,417	0	A	G	100.0%	235.1 / NA	64	pseudogene (24/468 nt)	rpsG	30S ribosomal protein S7
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (35/29);  total (35/29)

GCGCTGAGCCAGGGTCTCCAGCGCGCTGTATACGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGACCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACATTTAAGTTAAAACGTTTGGCCTTACTTAACGGAGAACCATT  >  NZ_CP009273/3467282‑3467538                                                                                                                                        |                                                                                                                          gcgcTGAGCCAGGGTCTCCAGCGCGCTGTATACGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGcc                                                                                                                         >  1:289858/1‑138 (MQ=255)            gggTCTCCAGCGCGCTGTATACGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGcgac                                                                                                              >  2:341607/1‑138 (MQ=255)            gggTCTCCAGCGCGCTGTATACGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGcgac                                                                                                              >  1:550619/1‑138 (MQ=255)               tctcCAGCGCGCTGTATACGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGacgacg                                                                                                          <  1:425283/139‑1 (MQ=255)                  ccAGCGCGCTGTATACGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTgg                                                                                                       >  2:395061/1‑139 (MQ=255)                   cAGCGCGCTGTATACGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTgg                                                                                                       >  2:169600/1‑138 (MQ=255)                    aGCGCGCTGTATACGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCa                                                                                                     <  2:511662/139‑1 (MQ=255)                    aGCGCGCTGTATACGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCa                                                                                                     <  2:486375/139‑1 (MQ=255)                        cgcTGTATACGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATgg                                                                                                  >  2:388851/1‑138 (MQ=255)                           tGTATACGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGaaa                                                                                               >  2:442375/1‑138 (MQ=255)                                 cGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTcc                                                                                         <  1:22764/138‑1 (MQ=255)                                 cGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTcc                                                                                         <  2:343697/138‑1 (MQ=255)                                      gATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgt                                                                                    <  1:341607/138‑1 (MQ=255)                                      gATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgt                                                                                    <  1:403006/138‑1 (MQ=255)                                      gATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgt                                                                                    <  2:8113/138‑1 (MQ=255)                                       aTTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAAt                                                                                                                      <  2:103405/103‑1 (MQ=255)                                       aTTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAAt                                                                                                                      >  1:103405/1‑103 (MQ=255)                                       aTTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgtt                                                                                   >  1:465044/1‑138 (MQ=255)                                       aTTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgtt                                                                                   >  2:175935/1‑138 (MQ=255)                                       aTTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgtt                                                                                   >  1:565465/1‑138 (MQ=255)                                       aTTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgtt                                                                                   >  2:806849/1‑138 (MQ=255)                                       aTTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgtt                                                                                   >  1:224763/1‑138 (MQ=255)                                       aTTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgtt                                                                                   >  1:374877/1‑138 (MQ=255)                                       aTTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgtt                                                                                   >  2:714886/1‑138 (MQ=255)                                       aTTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgtt                                                                                   >  2:729166/1‑138 (MQ=255)                                       aTTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgt                                                                                    >  1:190078/1‑137 (MQ=255)                                       aTTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgt                                                                                    <  2:190078/137‑1 (MQ=255)                                       aTTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGT‑GCATGGAAATACTCCGTTGTTaa                                                                                 >  1:795908/1‑139 (MQ=255)                                           agcagTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAAtt                                                                               >  1:296374/1‑138 (MQ=255)                                            gcagTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAAtt                                                                               >  1:85369/1‑137 (MQ=255)                                              agTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAg                                                                            >  1:752938/1‑138 (MQ=255)                                                  gATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTg                                                                       >  1:422483/1‑139 (MQ=255)                                                              tctaccatcAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGacgacg                                                                                                          >  1:123831/1‑92 (MQ=255)                                                              tctaccatcAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGacgacg                                                                                                          <  2:123831/92‑1 (MQ=255)                                                              tctaccatcAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgt                                                                                    >  1:19708/1‑114 (MQ=255)                                                              tctaccatcAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgt                                                                                    <  2:19708/114‑1 (MQ=255)                                                                  ccatcAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTa                                                           <  1:388851/135‑1 (MQ=255)                                                                     tcAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGagttt                                                    <  2:465044/139‑1 (MQ=255)                                                                        ggATCTTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgt                                                                                    >  1:430787/1‑104 (MQ=255)                                                                        ggATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCgttgt                                                                                    <  2:430787/104‑1 (MQ=255)                                                                          atatTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGa                                                                          <  2:595787/112‑1 (MQ=255)                                                                          atatTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGa                                                                          >  1:595787/1‑112 (MQ=255)                                                                            atTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCAt                                                                                                    >  1:137095/1‑84 (MQ=255)                                                                            atTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCAt                                                                                                    <  2:137095/84‑1 (MQ=255)                                                                            atTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGa                                             >  2:125260/1‑139 (MQ=255)                                                                             tttACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGa                                                                          >  2:358709/1‑109 (MQ=255)                                                                             tttACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGa                                                                          <  1:358709/109‑1 (MQ=255)                                                                             tttACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGa                                             >  2:779872/1‑138 (MQ=255)                                                                                                      aTCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCaa                                                                  <  1:465049/92‑1 (MQ=255)                                                                                                      aTCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCaa                                                                  >  2:465049/1‑92 (MQ=255)                                                                                                      aTCCGAACTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACATTTAAGTTAAAACGTTTGGcc                      <  1:169600/136‑1 (MQ=255)                                                                                                           aaCTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACAttt                                        >  1:71508/1‑113 (MQ=255)                                                                                                           aaCTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACAttt                                        <  2:71508/113‑1 (MQ=255)                                                                                                           aaCTTCGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACATTTAAGTTAAAACGTTTGGCCTTACTTaa              >  2:760513/1‑139 (MQ=255)                                                                                                                cGGATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGT‑GCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACATTTAAGTTAAAACGTTTGGCCTTACTTAACGga          <  2:795908/137‑1 (MQ=255)                                                                                                                 ggATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACATTTAAGTTAAAACGTTTGGCCTTACTTAACGgaga        <  1:85214/139‑1 (MQ=255)                                                                                                                 ggATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACATTTAAGTTAAAACGTTTGGCCTTACTTAACGgaga        <  2:752938/139‑1 (MQ=255)                                                                                                                 ggATCCGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCACGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACATTTAAGTTAAAACGTTTGGCCTTACTTAACGgag         <  2:509347/138‑1 (MQ=255)                                                                                                                 ggATCCGGCAGAATTTTACGCTGGACAATGACGCGACGACGTGGCATGTAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACATTTAAGTTAAAACGTGTGGCCTTACGTAACGgagt        <  2:65895/139‑2 (MQ=255)                                                                                                                      cGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACATTTAAGTTAAAACGTTTGGCCTTACTTAACGgag         >  1:448113/1‑133 (MQ=255)                                                                                                                      cGGCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACATTTAAGTTAAAACGTTTGGCCTTACTTAACGgag         <  2:448113/133‑1 (MQ=255)                                                                                                                       ggCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACATTTAAGTTAAAACGTTTGGCCTTACTTAACGGAGAACCAtt  <  2:565465/139‑1 (MQ=255)                                                                                                                        gCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACAttt                                        >  2:604862/1‑100 (MQ=255)                                                                                                                        gCAGAATTTTACGCTGGCCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACAttt                                        <  1:604862/100‑1 (MQ=255)                                                                                                                                        |                                                                                                                          GCGCTGAGCCAGGGTCTCCAGCGCGCTGTATACGATAGATTCAGCAGTAGATTTTTTACCATCTACCATCAGGATATTTACAAATTTAGCCAGCAGTTCTGATCCGAACTTCGGATCCGGCAGAATTTTACGCTGACCAATGACGCGACGACGTGGCATGGAAATACTCCGTTGTTAATTCAGGATTGTCCAAAACTCTACGAGTTTAGTTTGACATTTAAGTTAAAACGTTTGGCCTTACTTAACGGAGAACCATT  >  NZ_CP009273/3467282‑3467538

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑