Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,574,259	A→G	pseudogene (341/2937 nt)	yjiV →	pseudogene, conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,574,259	0	A	G	100.0%	236.8 / NA	64	pseudogene (341/2937 nt)	yjiV	pseudogene, conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (39/25);  total (39/25)

TATGTGTATGTGAACCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGAAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGCCGCAGGAGAGACCA  >  NC_000913/4574132‑4574384                                                                                                                                |                                                                                                                              tatgtgtatgtgAACCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTg                                                                                                                    <  1:397086/139‑1 (MQ=255)    gtgtatgtgAACCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCg                                                                                                                 >  2:1048767/1‑139 (MQ=255)         tgtgAACCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGaa                                                                                                            >  2:46632/1‑139 (MQ=255)             aaCCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATtct                                                                                                        >  1:645254/1‑139 (MQ=255)             aaCCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATtct                                                                                                        <  2:225532/139‑1 (MQ=255)              aCCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATtctc                                                                                                       >  2:1263558/1‑139 (MQ=255)               ccAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTctct                                                                                                      >  2:671436/1‑139 (MQ=255)               ccAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTctct                                                                                                      >  1:169584/1‑139 (MQ=255)                 aGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATtct                                                                                                        <  2:1167942/135‑1 (MQ=255)                 aGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATtct                                                                                                        >  1:1167942/1‑135 (MQ=255)                  gCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTATAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTg                                                                                                   >  2:797958/1‑139 (MQ=255)                    gACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCa                                                                                                 <  1:46632/139‑1 (MQ=255)                      cAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAgg                                                                                               <  1:67351/139‑1 (MQ=255)                      cAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAgg                                                                                               <  1:1048767/139‑1 (MQ=255)                        aaaTTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGAt                                                                                             <  1:230350/139‑1 (MQ=255)                               gACTGTGGCAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTAc                                                                                      <  2:652963/139‑1 (MQ=255)                               gACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTAc                                                                                      <  2:469449/139‑1 (MQ=255)                                    tgGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGtt                                                                                 <  1:114247/139‑1 (MQ=255)                                              gTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACg                                                                       >  1:1043380/1‑139 (MQ=255)                                              gTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACg                                                                       >  1:39414/1‑139 (MQ=255)                                                         tGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAgaagaa                                                            >  1:253387/1‑139 (MQ=255)                                                         tGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAgaagaa                                                            >  1:1078129/1‑139 (MQ=255)                                                           cATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGaaaa                                                          <  2:918742/139‑1 (MQ=255)                                                           cATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGaaaa                                                          >  1:1132945/1‑139 (MQ=255)                                                           cATTCTGTAATGACTGTAATGAGTCTCAGCTTCCGCCACTGGACAACAAGGGCAAACTAGTCCAGTGGGGCAATAAACGTGGTGATGAATCCTCTGTGCAGGATGAAGTACCTATTGAAATTGACGCTACAGAAGgaaa                                                          >  1:278128/1‑139 (MQ=255)                                                                          gTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATtct                                                                                                        <  2:1225668/78‑1 (MQ=255)                                                                          gTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATtct                                                                                                        >  1:1225668/1‑78 (MQ=255)                                                                          gTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACa                                                                            <  2:77536/106‑1 (MQ=255)                                                                          gTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACa                                                                            >  1:77536/1‑106 (MQ=255)                                                                            aaTGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACa                                                                            <  1:1279246/104‑1 (MQ=255)                                                                            aaTGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACa                                                                            >  2:1279246/1‑104 (MQ=255)                                                                            aaTGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACa                                         >  2:1066509/1‑139 (MQ=255)                                                                            aaTGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTATTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACa                                         >  1:943466/1‑139 (MQ=255)                                                                                aGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGttt                                     >  1:185327/1‑139 (MQ=255)                                                                                 gCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAaga                                              <  1:353710/129‑1 (MQ=255)                                                                                 gCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAaga                                              >  2:353710/1‑129 (MQ=255)                                                                                 gCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGtttt                                    >  1:1260087/1‑139 (MQ=255)                                                                                 gCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGtttt                                    >  1:890962/1‑139 (MQ=255)                                                                                  ccTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTAc                                                                                      >  2:608987/1‑88 (MQ=255)                                                                                  ccTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTAc                                                                                      <  1:608987/88‑1 (MQ=255)                                                                                  ccTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTc                                   >  1:140099/1‑139 (MQ=255)                                                                                  ccTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTc                                   >  1:792819/1‑139 (MQ=255)                                                                                  ccTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTc                                   >  1:280407/1‑139 (MQ=255)                                                                                   cTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCa                                  >  2:1200678/1‑139 (MQ=255)                                                                                     cATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGAt                                                                                             <  1:628130/78‑1 (MQ=255)                                                                                     cATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGAt                                                                                             >  2:628130/1‑78 (MQ=255)                                                                                     cATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGc                                >  1:468743/1‑139 (MQ=255)                                                                                     cATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGc                                <  2:1260087/139‑1 (MQ=255)                                                                                       tcttctGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCt                              <  1:797958/139‑1 (MQ=255)                                                                                          tctGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCg                                                     >  2:740019/1‑113 (MQ=255)                                                                                          tctGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCg                                                     <  1:740019/113‑1 (MQ=255)                                                                                            tGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTAc                                                                                      >  2:1269522/1‑78 (MQ=255)                                                                                            tGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTAc                                                                                      <  1:1269522/78‑1 (MQ=255)                                                                                            tGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGtt                         >  1:127791/1‑139 (MQ=255)                                                                                                  gggACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGattat                   <  2:140099/139‑1 (MQ=255)                                                                                                    gACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTg                 >  2:659672/1‑139 (MQ=255)                                                                                                    gACAAAAAGGGCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTg                 >  1:57433/1‑139 (MQ=255)                                                                                                             ggCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGCCGCAGgag        >  2:78857/1‑139 (MQ=255)                                                                                                              gCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGTAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGCCg              <  2:647435/132‑1 (MQ=255)                                                                                                              gCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGTAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGCCg              >  1:647435/1‑132 (MQ=255)                                                                                                              gCAAACTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGCCGCAGgaga       >  1:771619/1‑139 (MQ=255)                                                                                                                   cTAGTCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGCCGCAGGAGAGACCa  <  1:671436/139‑1 (MQ=255)                                                                                                                       tCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTg                                                                                   <  1:470856/54‑1 (MQ=255)                                                                                                                       tCCAGTGGGGAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTg                                                                                   >  2:470856/1‑54 (MQ=255)                                                                                                                             ggggAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGc                                <  1:1184748/99‑1 (MQ=255)                                                                                                                             ggggAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGc                                >  2:1184748/1‑99 (MQ=255)                                                                                                                                |                                                                                                                              TATGTGTATGTGAACCAGCGACAAAATTGTGACTGTGGAAGCCCTGTATACGAAGTTGCATTCTGTAATGATTGTAATGAGCCTCATCTTCTGGCACGGGACAAAAAGGGCAAACTAGTCCAGTGGGAAAATAAAGGTGGCGATGAATTCTCTTTGCAGGATGAAGTACCTGTTGAACATGACGCTACAGAAGAAAAAGTCGAAAAAGAGAACAGTTTTCAGCCTCCGTTGATTATTGCCGCAGGAGAGACCA  >  NC_000913/4574132‑4574384

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑