Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,500,060	C→T	pseudogene (475/942 nt)	yjgX ←	pseudogene fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,500,060	0	C	T	100.0%	175.4 / NA	54	pseudogene (475/942 nt)	yjgX	pseudogene fragment
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (28/26);  total (28/26)

AATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGCTAGGAGTTAAGGCTGTCACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGA  >  NC_000913/4499925‑4500194                                                                                                                                        |                                                                                                                                       aaTGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTtaca                                                                                                                                     <  2:578843/139‑1 (MQ=255) aaTGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTtaca                                                                                                                                     <  2:690817/139‑1 (MQ=255)               cGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGGTGCTGGCGAGGTAACAGGTAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgag                                                                                                                       <  2:1334203/139‑1 (MQ=255)               cGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATg                                                                                                                         >  1:778981/1‑137 (MQ=255)               cGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATg                                                                                                                         <  2:778981/137‑1 (MQ=255)                    aaGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTtac                                                                                                                                      >  1:59102/1‑119 (MQ=255)                    aaGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTtac                                                                                                                                      <  2:59102/119‑1 (MQ=255)                       gATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCcatc                                                                                                               <  2:825763/139‑1 (MQ=255)                                 aGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGa                                                                                                                           >  1:735969/1‑117 (MQ=255)                                 aGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGa                                                                                                                           <  2:735969/117‑1 (MQ=255)                                   cTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGaaa                                                                                                   >  2:598301/1‑139 (MQ=255)                                      gCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAAtt                                                                                                >  2:711280/1‑139 (MQ=255)                                      gCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAAtt                                                                                                <  1:593667/139‑1 (MQ=255)                                      gCCAAGAAACTTCTCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATAATTCGGGGATACTGCTCTAGGTAATTATTCTGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAATCTATCATGTGCAGGAAAAtt                                                                                                >  2:994472/1‑139 (MQ=255)                                                ttATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCg                                                                                         <  1:39777/136‑1 (MQ=255)                                                ttATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCg                                                                                         >  2:39777/1‑136 (MQ=255)                                                   tCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAgg                                                                                   <  2:310361/139‑1 (MQ=255)                                                                  cTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGAt                                                                                                                          <  1:477119/85‑1 (MQ=255)                                                                  cTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGAt                                                                                                                          >  2:477119/1‑85 (MQ=255)                                                                  cTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTCGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAgcg                                                                    >  2:185801/1‑139 (MQ=255)                                                                  cTGGCGAGGTAACAGGCAATTTTTCGAGGATATTGCTCCAGGTACTTATTCGGTTAGGAGGTAAGGCTGTTACACGGATTTGGAGGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAgcg                                                                    >  2:913343/1‑139 (MQ=255)                                                                    ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTacac                                                                                                                                    <  1:1382913/73‑1 (MQ=255)                                                                    ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTacac                                                                                                                                    >  2:1382913/1‑73 (MQ=255)                                                                    ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCa                                                                  >  1:389114/1‑139 (MQ=255)                                                                          gTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGga                                                                                       <  2:176358/112‑1 (MQ=255)                                                                          gTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGga                                                                                       >  1:176358/1‑112 (MQ=255)                                                                          gTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAg                                                                      >  1:405199/1‑129 (MQ=255)                                                                          gTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAg                                                                      <  2:405199/129‑1 (MQ=255)                                                                          gTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCt                                                            >  1:802294/1‑139 (MQ=255)                                                                                    aTTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGt                                                               >  2:453484/1‑126 (MQ=255)                                                                                    aTTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGt                                                               <  1:453484/126‑1 (MQ=255)                                                                                    aTTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTa                                                  <  1:711280/139‑1 (MQ=255)                                                                                    aTTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTa                                                  >  1:392938/1‑139 (MQ=255)                                                                                     tttttCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGtt                                                         >  2:1368357/1‑131 (MQ=255)                                                                                     tttttCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGtt                                                         <  1:1368357/131‑1 (MQ=255)                                                                                         tCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTaacaac                                             <  2:389114/139‑1 (MQ=255)                                                                                             ggATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGtt                                         >  2:711206/1‑139 (MQ=255)                                                                                               aTACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGAt                                                                                                                          >  2:463124/1‑56 (MQ=255)                                                                                               aTACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGAt                                                                                                                          <  1:463124/56‑1 (MQ=255)                                                                                                        cAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCAt                                   >  2:879722/1‑134 (MQ=255)                                                                                                        cAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCAt                                   <  1:879722/134‑1 (MQ=255)                                                                                                          ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgag                                                                                                                       <  2:1460387/48‑1 (MQ=255)                                                                                                          ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgag                                                                                                                       >  1:1460387/1‑48 (MQ=255)                                                                                                          ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCGTGTGCAGGAAAATTATCtt                                                                                           >  2:47775/1‑76 (MQ=255)                                                                                                          ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCGTGTGCAGGAAAATTATCtt                                                                                           <  1:47775/76‑1 (MQ=255)                                                                                                           gTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTa                           >  1:19856/1‑139 (MQ=255)                                                                                                               ttattCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCAc                                                                 <  1:1359347/97‑1 (MQ=255)                                                                                                               ttattCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCAc                                                                 >  2:1359347/1‑97 (MQ=255)                                                                                                                    cggttAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGgaagcg                  <  1:1215975/135‑1 (MQ=255)                                                                                                                    cGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGgaagcg                  >  1:1528264/1‑139 (MQ=255)                                                                                                                         aGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTcc                                                      <  1:233602/98‑1 (MQ=255)                                                                                                                         aGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTcc                                                      >  2:233602/1‑98 (MQ=255)                                                                                                                            aGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGa                                                                                                     >  1:149892/1‑48 (MQ=255)                                                                                                                            aGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGa                                                                                                     <  2:149892/48‑1 (MQ=255)                                                                                                                                  ggCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCtt    <  2:236667/139‑1 (MQ=255)                                                                                                                                   gCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCtt        >  1:630016/1‑134 (MQ=255)                                                                                                                                   gCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCtt        <  2:630016/134‑1 (MQ=255)                                                                                                                                    cTGTTACATGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACTTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGa  <  1:913343/139‑1 (MQ=255)                                                                                                                                        |                                                                                                                                       AATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGCTAGGAGTTAAGGCTGTCACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCGAAGCTGCCTTTCTTGA  >  NC_000913/4499925‑4500194

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑