Predicted mutation
evidence seq id position mutation freq annotation gene description
RA AP009048 3,824,378 2 bp→AA 100% pseudogene (513‑514/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AP0090483,824,3780GA100.0% 183.8 / NA 62pseudogene (513/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/34);  total (28/34)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
*AP0090483,824,3790GA100.0% 185.1 / NA 62pseudogene (514/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/34);  total (28/34)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGAC  >  AP009048/3824313‑3824440
                                                                 ||                                                             
cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                                           >  1:4091924/1‑71 (MQ=255)
    aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                       >  1:2765275/1‑71 (MQ=255)
        cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                   <  1:2354774/71‑1 (MQ=255)
         aacccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGa                                                  <  1:760545/68‑1 (MQ=255)
          acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                                 <  1:3916880/69‑1 (MQ=255)
            ccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                       <  1:415317/63‑1 (MQ=255)
               aTGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                            >  1:286995/1‑71 (MQ=255)
               aTGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                            >  1:2788350/1‑71 (MQ=255)
                tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                                           >  1:2777044/1‑55 (MQ=255)
                tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                           <  1:1625172/71‑1 (MQ=255)
                tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                           >  1:309222/1‑71 (MQ=255)
                tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                           <  1:1810266/71‑1 (MQ=255)
                tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                           <  1:2209204/71‑1 (MQ=255)
                tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt                                            >  1:2818997/1‑70 (MQ=255)
                  aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                          <  1:4200508/70‑1 (MQ=255)
                  aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                          <  1:32826/70‑1 (MQ=255)
                  aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                          >  1:2778388/1‑70 (MQ=255)
                  aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                          <  1:502093/70‑1 (MQ=255)
                   aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                        <  1:689048/71‑1 (MQ=255)
                    aGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGa                                         >  1:2159003/1‑69 (MQ=255)
                      ggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAc                                     <  1:2703001/71‑1 (MQ=255)
                       gATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                                    <  1:4224753/71‑1 (MQ=255)
                         tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                        <  1:1463095/65‑1 (MQ=255)
                          ggTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGa                                         <  1:2484374/63‑1 (MQ=255)
                           gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                   <  1:4472966/52‑1 (MQ=255)
                            tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                           >  1:2286174/1‑59 (MQ=255)
                               ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                            <  1:3503062/71‑1 (MQ=255)
                                    gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                       >  1:4060063/1‑71 (MQ=255)
                                     tttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                      <  1:116376/71‑1 (MQ=255)
                                      ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                      >  1:2135402/1‑70 (MQ=255)
                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                                 >  1:443394/1‑42 (MQ=19)
                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                                 <  1:1477228/42‑1 (MQ=19)
                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                           >  1:727257/1‑48 (MQ=25)
                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                        >  1:3504584/1‑51 (MQ=255)
                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg                              <  1:585111/61‑1 (MQ=255)
                                       tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg                              <  1:3258081/61‑1 (MQ=255)
                                        cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                    <  1:2209524/70‑1 (MQ=255)
                                        cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                    <  1:4021500/70‑1 (MQ=255)
                                          gTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                            >  1:78123/1‑60 (MQ=255)
                                           tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg                <  1:2989136/71‑1 (MQ=255)
                                            cGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                        <  1:1820818/46‑1 (MQ=25)
                                            cGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg                >  1:1787282/1‑70 (MQ=255)
                                               taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg            >  1:1139677/2‑71 (MQ=255)
                                                aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg            >  1:3243315/1‑70 (MQ=255)
                                                 ttGTAAACGGTGAAGCAATTTGCGATCTGGAATAc                                              >  1:1591977/1‑35 (MQ=16)
                                                 ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACAt                 <  1:3321201/64‑1 (MQ=255)
                                                 ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg            >  1:175693/1‑69 (MQ=255)
                                                      aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGCCCGACATGAACGTAGtgat     >  1:498858/1‑71 (MQ=255)
                                                      aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa               <  1:2565892/61‑1 (MQ=255)
                                                      aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat     <  1:4065390/71‑1 (MQ=255)
                                                      aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat     <  1:231623/71‑1 (MQ=255)
                                                      aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat     <  1:3992509/71‑1 (MQ=255)
                                                      aaCGGTGAAGCAATTTGCGATCTGGAATACGTCGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat     <  1:3842845/71‑1 (MQ=255)
                                                       aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                            >  1:4531103/1‑47 (MQ=37)
                                                       aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGAc                   >  1:684489/1‑56 (MQ=255)
                                                       aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg    <  1:1045025/71‑1 (MQ=255)
                                                       aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat     >  1:2686611/1‑70 (MQ=255)
                                                       aCGGTGAAGCAATTTGAGATCTGGAATACGTTGAAGACTCAGCCGc                             >  1:4247706/1‑46 (MQ=255)
                                                        cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTTAGCCGCAGACACCGACATGAACGTAGtgatga   >  1:233203/1‑71 (MQ=255)
                                                         ggtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc  <  1:3639576/68‑1 (MQ=255)
                                                         ggtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc  >  1:3672291/4‑71 (MQ=255)
                                                           tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg            <  1:1286563/58‑1 (MQ=255)
                                                                 ||                                                             
CTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGAC  >  AP009048/3824313‑3824440

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: