Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	4,007,539	G→A	pseudogene (367/393 nt)	yhiK →	ECK3474:JW5674:b3489; hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,007,539	0	G	A	100.0%	143.9 / NA	48	pseudogene (367/393 nt)	yhiK	ECK3474:JW5674:b3489; hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (17/31);  total (17/31)

GGTATTATGGGGCTAAATTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAGGGCTTAGTTGTTTTCAACTACATTAAAACTCCATGAATACGGTGGTATGTCTTTTTAAT  >  W3110S.gb/4007473‑4007598                                                                   |                                                            ggTATTATGGGGCTAAATTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCt                                                         >  1:542096/1‑71 (MQ=255)  gTATTATGGGGCTAAATTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCtt                                                        <  1:1503931/71‑1 (MQ=255)  gTATTATGGGGCTAAATTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCtt                                                        <  1:2969009/71‑1 (MQ=255)  gTATTATGGGGCTAAATTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCt                                                         >  1:3584575/1‑70 (MQ=255)  gTATTATGGGGCTAAATTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCt                                                         >  1:3681258/1‑70 (MQ=255)    attatGGGGCTAAATTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAg                                                      >  1:2992609/1‑71 (MQ=255)       atGGGGCTAAATTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAgttg                                                   >  1:314548/1‑71 (MQ=255)       atGGGGCTAAATTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAgttg                                                   >  1:1563225/1‑71 (MQ=255)       atGGGGATAAATTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAgttg                                                   >  1:8626/1‑71 (MQ=255)        tGGGGCTAAATTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAgttg                                                   <  1:4054197/70‑1 (MQ=255)                aaTTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAAc                                           <  1:2595433/70‑1 (MQ=255)                aaTTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAAc                                           >  1:424885/1‑70 (MQ=255)                 aTTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTa                                         <  1:4228335/71‑1 (MQ=255)                 aTTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTAGTTTTCAACTa                                         <  1:3050242/71‑1 (MQ=255)                    cccTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACAt                                      >  1:249031/1‑71 (MQ=255)                    cccTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACAt                                      >  1:3898756/1‑71 (MQ=255)                         aaggaagCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTaa                                   <  1:2680705/69‑1 (MQ=255)                         aaggaagCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTaa                                   <  1:3771264/69‑1 (MQ=255)                         aaggaagCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTaa                                   <  1:146556/69‑1 (MQ=255)                         aaggaagCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTaa                                   <  1:3225461/69‑1 (MQ=255)                            gaagCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTc                              <  1:3362887/71‑1 (MQ=255)                            gaagCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTc                              <  1:3359186/71‑1 (MQ=255)                            gaagCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTc                              <  1:855499/71‑1 (MQ=255)                            gaagCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTc                              <  1:1180946/71‑1 (MQ=255)                              agCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCa                            >  1:3596063/1‑71 (MQ=255)                              agCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCa                            >  1:872544/1‑71 (MQ=255)                              agCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCa                            >  1:977635/1‑71 (MQ=255)                              agCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCa                            >  1:1183229/1‑71 (MQ=255)                              agCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCa                            >  1:1221209/1‑71 (MQ=255)                              agCACGTGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCa                            >  1:2365823/1‑71 (MQ=255)                                    tGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAgttgt                                                  <  1:452808/43‑1 (MQ=255)                                    tGATAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGTTTTCAACTa                                         <  1:4258397/52‑1 (MQ=255)                                      aTAAAAATAATAAAATAATTTATTCCTCAAGGCTTAGTTGttt                                                <  1:3026384/43‑1 (MQ=255)                                         aaaataataaaataatTTATTCCTCAAGGCTTAGTTGTTTTc                                              <  1:3304982/42‑1 (MQ=255)                                          aaataataaaataatTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCATGAATACggtgg                <  1:966079/71‑1 (MQ=255)                                          aaataataaaataatTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCATGAATACggtgg                <  1:1277323/71‑1 (MQ=255)                                          aaataataaaataatTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCATGAATACggtgg                <  1:432020/71‑1 (MQ=255)                                           aataataaaataatTTATTCCTCAAGGCTTAGTTGTTTTCaa                                            >  1:3805530/1‑42 (MQ=255)                                           aataataaaataatTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCATGAATACggtgg                <  1:1127165/70‑1 (MQ=255)                                            ataataaaataatTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCATGAATACGGTGGTa              <  1:1710350/71‑1 (MQ=255)                                             taataaaataatTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTaa                                   <  1:2656924/49‑1 (MQ=255)                                                     taatTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCATGAATACGGTGGTATGTCttttt     <  1:3911389/71‑1 (MQ=255)                                                       atTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCATGAATACGGTGGTATGTCTTTTTaa   <  1:2083038/71‑1 (MQ=255)                                                       atTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCATGAATACGGTGGTATGTCTTTTTaa   <  1:396999/71‑1 (MQ=255)                                                       atTTATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCATGAATACGGTGGTATGTCTTTTTa    <  1:4318464/70‑1 (MQ=255)                                                        tttATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCATg                          <  1:2796440/47‑1 (MQ=255)                                                        tttATTCCTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCATGAATACGGTGGTATGTCTTTTTAAt  <  1:327373/71‑1 (MQ=255)                                                               cTCAAGGCTTAGTTGTTTTCAACTACATTAAAACTCCATGAATACGGTGGTATGTCTTTTTAAt  <  1:1186890/64‑1 (MQ=255)                                                                   |                                                            GGTATTATGGGGCTAAATTCCCTGAAGGAAGCACGTGATAAAAATAATAAAATAATTTATTCCTCAGGGCTTAGTTGTTTTCAACTACATTAAAACTCCATGAATACGGTGGTATGTCTTTTTAAT  >  W3110S.gb/4007473‑4007598

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑