Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,824,410 T→A 100% pseudogene (543/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,4100TA100.0% 350.4 / NA 114pseudogene (543/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (42/72);  total (42/72)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

Only 100 of 115 total aligned reads displayed.

TAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGAC  >  W3110S.gb/3824343‑3824475
                                                                   |                                                                 
tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc                                                                <  1:2234533/71‑1 (MQ=255)
  gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGc                                                              <  1:2720575/71‑1 (MQ=255)
    cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg                                                               >  1:3025637/1‑68 (MQ=255)
     gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga                                                           <  1:7771109/71‑1 (MQ=255)
     gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga                                                           <  1:6906349/71‑1 (MQ=255)
     gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                                                             >  1:2225744/1‑69 (MQ=255)
      cAGTTTCTGTCGGTATTGTAAACTGTGAAGCAATTTGCGATCTTTAATACGTTGAAGACTCAGCCGCagag                                                          <  1:3740734/71‑1 (MQ=255)
      cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                                                          <  1:4233017/71‑1 (MQ=255)
      cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                                                          <  1:4794930/71‑1 (MQ=255)
      cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                                                          <  1:5058258/71‑1 (MQ=255)
       aGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga                                                         >  1:2589623/1‑71 (MQ=255)
        gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                                                        >  1:7425069/1‑71 (MQ=255)
        gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                                                        >  1:5687211/1‑71 (MQ=255)
        gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                                                        >  1:1883730/1‑71 (MQ=255)
           tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                                                        >  1:2439976/1‑68 (MQ=255)
               tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACAt                                                  >  1:6175232/1‑70 (MQ=255)
               tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg                                                 <  1:1671366/71‑1 (MQ=255)
               tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg                                                 <  1:1680565/71‑1 (MQ=255)
               tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCACATg                                                 <  1:3435336/70‑1 (MQ=255)
                cGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                                                        >  1:4989220/1‑63 (MQ=255)
                 ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa                                                <  1:2624338/67‑1 (MQ=255)
                   taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg                                             >  1:7038369/2‑71 (MQ=255)
                     ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa                                           <  1:3721873/71‑1 (MQ=255)
                       gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAg                                          <  1:7020579/67‑1 (MQ=255)
                        taaaCGGTGAAGCAATTTGCGATTTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                         <  1:4663940/68‑1 (MQ=255)
                        taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCTCAGAGACCGACATGAACGTAGt                                         <  1:6996966/68‑1 (MQ=255)
                        taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                                       <  1:1410926/54‑1 (MQ=255)
                        taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                                                       <  1:30812/54‑1 (MQ=255)
                        taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg                                        <  1:1857386/69‑1 (MQ=255)
                        taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                         <  1:290579/68‑1 (MQ=255)
                        taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                         <  1:5813970/68‑1 (MQ=255)
                         aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga                                       >  1:3040612/2‑71 (MQ=255)
                         aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg                                        <  1:2235361/69‑1 (MQ=255)
                          aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCag                                                            >  1:5588589/1‑49 (MQ=37)
                          aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                                               >  1:845361/1‑62 (MQ=255)
                          aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAg                                          <  1:7497985/67‑1 (MQ=255)
                          aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAg                                          <  1:464650/67‑1 (MQ=255)
                           aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa                                               >  1:3742015/1‑61 (MQ=255)
                           aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg                                     <  1:5144727/71‑1 (MQ=255)
                           aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat                                      >  1:3047692/1‑70 (MQ=255)
                            cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg                                                      <  1:6044309/53‑1 (MQ=255)
                            cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg                                                      <  1:5649620/53‑1 (MQ=255)
                            cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                                                     >  1:4620357/1‑54 (MQ=255)
                            cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatga                                    <  1:6593615/71‑1 (MQ=255)
                            cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatga                                    >  1:4519624/1‑71 (MQ=255)
                               tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg                                        <  1:1392341/63‑1 (MQ=255)
                               tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAcc                                  <  1:7178200/69‑1 (MQ=255)
                               tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAcc                                  <  1:1311965/69‑1 (MQ=255)
                               tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg                                 <  1:2323506/70‑1 (MQ=255)
                               tgAAGCAATTTGCGATCTGGAATACGTTAAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg                                 <  1:5467148/70‑1 (MQ=255)
                               tgAAGCAATTTGCGATCTGGAATACGTTAAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg                                 <  1:1878500/70‑1 (MQ=255)
                                gAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                                                             <  1:6494900/42‑1 (MQ=37)
                                gAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAcc                                  >  1:2273193/1‑69 (MQ=255)
                                gAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg                                 >  1:3519890/1‑70 (MQ=255)
                                gAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg                                 >  1:5830675/1‑70 (MQ=255)
                                    caatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGAc                            <  1:5018040/68‑1 (MQ=255)
                                    caatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGAc                            >  1:243665/4‑71 (MQ=255)
                                     aatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg                                        <  1:7634685/56‑1 (MQ=255)
                                     aatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                         <  1:2990318/55‑1 (MQ=255)
                                     aatttGCGATCCGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACg                           <  1:560271/69‑1 (MQ=255)
                                       tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg                                                      <  1:2957589/42‑1 (MQ=255)
                                       tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg                                                      <  1:6518847/42‑1 (MQ=255)
                                         tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                         >  1:6753899/1‑53 (MQ=255)
                                         tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgc                        <  1:6345514/70‑1 (MQ=255)
                                           cGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcgc                      <  1:1624845/70‑1 (MQ=255)
                                             aTCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt                                            <  1:5021709/46‑1 (MQ=255)
                                             aTCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt                                            <  1:742287/46‑1 (MQ=255)
                                              tCTGTAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt                                            <  1:7180164/45‑1 (MQ=255)
                                              tCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatca                  >  1:7793280/1‑71 (MQ=255)
                                               cTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa                               <  1:3196342/57‑1 (MQ=255)
                                               cTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatcat                 >  1:7302873/1‑71 (MQ=255)
                                                tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCAtt                >  1:754293/1‑71 (MQ=255)
                                                tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCAACAtt                >  1:7052146/1‑71 (MQ=255)
                                                  gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg                                 >  1:146092/1‑52 (MQ=255)
                                                  gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatcat                 <  1:3170898/68‑1 (MQ=255)
                                                  gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatca                  <  1:2605995/67‑1 (MQ=255)
                                                  gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCAtt                <  1:1003468/69‑1 (MQ=255)
                                                  gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCAtt                <  1:3921851/69‑1 (MQ=255)
                                                  gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg               >  1:3874507/1‑70 (MQ=255)
                                                  gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg               <  1:822694/70‑1 (MQ=255)
                                                  gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg               <  1:2450860/70‑1 (MQ=255)
                                                    aTACGTTGAAGAGTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAg            >  1:5525151/1‑71 (MQ=255)
                                                    aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAg            >  1:4468822/1‑71 (MQ=255)
                                                    aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAg            <  1:3786668/71‑1 (MQ=255)
                                                    aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAg            >  1:2928124/1‑71 (MQ=255)
                                                    aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAg            >  1:937414/1‑71 (MQ=255)
                                                       cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAg                              >  1:6080057/1‑50 (MQ=255)
                                                       cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTg          <  1:5656379/70‑1 (MQ=255)
                                                       cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTg          >  1:5258248/1‑70 (MQ=255)
                                                         ttGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGTCCGAAGACGGGCGCATCATTGAAGTGCAg       <  1:1320959/71‑1 (MQ=255)
                                                         ttGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCCTCATTg               <  1:1015080/63‑1 (MQ=255)
                                                         ttGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg               <  1:4581384/63‑1 (MQ=255)
                                                         ttGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg               <  1:3641131/63‑1 (MQ=255)
                                                         ttGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg               <  1:2341313/63‑1 (MQ=255)
                                                          tGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCTTTGAAGTGc         <  1:637708/68‑1 (MQ=255)
                                                           gAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg                                     <  1:6589601/39‑1 (MQ=255)
                                                           gAAGACTCAGCCGCAGAGACCGACATGAACGTAGt                                         <  1:2945127/35‑1 (MQ=255)
                                                             aGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGa   <  1:178010/71‑1 (MQ=255)
                                                               aCTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCa        >  1:6924680/1‑64 (MQ=255)
                                                                ctcaGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgc                        <  1:6154388/47‑1 (MQ=255)
                                                                   |                                                                 
TAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGAC  >  W3110S.gb/3824343‑3824475

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: