Predicted mutation
evidence seq id position mutation freq annotation gene description
RA AP009048 3,824,512 T→C 100% pseudogene (647/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AP0090483,824,5120TC100.0% 254.9 / NA 73pseudogene (647/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (31/42);  total (31/42)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGAGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAA  >  AP009048/3824444‑3824577
                                                                    |                                                                  
aGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCt                                                                  <  1:3358386/71‑1 (MQ=255)
 gACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCtt                                                                 <  1:2609661/71‑1 (MQ=255)
   cGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttgt                                                               <  1:3810848/71‑1 (MQ=255)
    gggCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttgt                                                               <  1:1823213/70‑1 (MQ=255)
      gcgcATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTgg                                                            <  1:4174105/71‑1 (MQ=255)
      gcgcATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTgg                                                            >  1:2819301/1‑71 (MQ=255)
         catcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCAGTTCACCCATGAAGAGCTACTCACCTTGTTGGcgc                                                         >  1:3207136/1‑69 (MQ=255)
          atcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGcgct                                                        <  1:863388/71‑1 (MQ=255)
          atcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATCAAGAGCTACTCACCttgt                                                               <  1:3652150/64‑1 (MQ=255)
           tcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTg                                                       >  1:449813/1‑71 (MQ=255)
            catTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTgg                                                      >  1:13928/1‑71 (MQ=255)
             atTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGcgc                                                         <  1:4016752/67‑3 (MQ=255)
             atTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTg                                                       >  1:4548516/1‑69 (MQ=255)
               tGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTg                                                       >  1:167669/1‑67 (MQ=255)
               tGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGccc                                                   >  1:1538814/1‑71 (MQ=255)
                gAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTtggccctggccc                                                   <  1:4046639/70‑1 (MQ=255)
                 aaGTGCTGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg                                                  <  1:2647979/70‑1 (MQ=255)
                  aGTGCAGGGGACGGCAGAAGGCGAGCCGTTAACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAg                                               >  1:2886364/1‑71 (MQ=255)
                   gTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgg                                              <  1:923932/71‑1 (MQ=255)
                   gTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgg                                              <  1:1994542/71‑1 (MQ=255)
                     gCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCtt                                                                 >  1:3867788/1‑51 (MQ=255)
                     gCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgggg                                            >  1:1480887/1‑71 (MQ=255)
                       aGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAggggga                                          <  1:4378484/71‑3 (MQ=255)
                       aGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAggggga                                          <  1:1522694/71‑3 (MQ=255)
                        ggggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAg                                               <  1:4226278/65‑1 (MQ=255)
                        ggggACGGCAGAAGGCGAGCCGTTAACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgggggaa                                         <  1:3837257/71‑4 (MQ=255)
                         gggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgggtga                                          <  1:2598685/69‑4 (MQ=255)
                           gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGa                                                 <  1:1499694/61‑1 (MQ=255)
                           gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcg                                       <  1:2910146/71‑1 (MQ=255)
                             cGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaa                                     >  1:3978112/1‑71 (MQ=255)
                             cGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaa                                     <  1:4209245/71‑1 (MQ=255)
                                cAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGc                                                     >  1:339659/1‑52 (MQ=255)
                                 aGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATcc                                  <  1:1606050/70‑1 (MQ=255)
                                  gAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAt                                >  1:2522061/1‑71 (MQ=255)
                                   aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAtt                               >  1:1012633/1‑71 (MQ=255)
                                       cGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAggg                                             >  1:2554024/1‑52 (MQ=255)
                                         aGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg                                                  <  1:3843503/46‑1 (MQ=255)
                                         aGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGc                          <  1:689904/70‑1 (MQ=255)
                                           ccGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg                                                  <  1:3549784/44‑1 (MQ=38)
                                            cGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATcc                                  <  1:1045066/59‑1 (MQ=255)
                                             gTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGa                                                 >  1:827105/1‑43 (MQ=38)
                                             gTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGc                     <  1:85134/71‑1 (MQ=255)
                                              ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCa                    <  1:2191066/71‑1 (MQ=255)
                                                cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                   >  1:3637988/1‑70 (MQ=255)
                                                cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                   <  1:550185/70‑1 (MQ=255)
                                                 aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAAGCGAATCCATTGTAGCGACGCAGaa                 <  1:2276915/71‑1 (MQ=255)
                                                   ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                   <  1:4215171/67‑1 (MQ=255)
                                                   ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAgg               >  1:1521965/1‑71 (MQ=255)
                                                    cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcga                                      >  1:275696/1‑47 (MQ=255)
                                                    cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAg                                               >  1:4060126/1‑37 (MQ=38)
                                                     aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcga                                      >  1:640054/1‑46 (MQ=255)
                                                     aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGt                             <  1:3244514/55‑1 (MQ=255)
                                                     aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGt                             <  1:4021393/55‑1 (MQ=255)
                                                     aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcg             >  1:412064/1‑71 (MQ=255)
                                                      tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGa                        >  1:4157536/1‑59 (MQ=255)
                                                      tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGa                        >  1:2041695/1‑59 (MQ=255)
                                                      tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggc              <  1:1080183/69‑1 (MQ=255)
                                                      tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAggggg                                           <  1:3134011/39‑2 (MQ=37)
                                                       gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCg                         <  1:2722991/57‑1 (MQ=255)
                                                       gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa                 <  1:948776/65‑1 (MQ=255)
                                                        aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGCATCCATTGTAGCGACGCAGAAGgcggcg          >  1:94244/1‑71 (MQ=255)
                                                        aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCg                         <  1:2717821/56‑1 (MQ=255)
                                                        aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGa                        >  1:3403402/1‑57 (MQ=255)
                                                        aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg          <  1:1012166/71‑1 (MQ=255)
                                                         agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaa                                     <  1:2067287/43‑1 (MQ=25)
                                                         agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcggc           >  1:3883829/1‑69 (MQ=255)
                                                          gagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCt        <  1:1254803/71‑1 (MQ=255)
                                                          gagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCt        >  1:3530465/1‑71 (MQ=255)
                                                           agCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCt        >  1:733407/1‑70 (MQ=255)
                                                               aCTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCa    >  1:2816843/1‑70 (MQ=255)
                                                                cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCa    <  1:3865904/69‑1 (MQ=255)
                                                                 tCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGc                          <  1:1259767/46‑1 (MQ=255)
                                                                 tCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCaaa  >  1:3890538/1‑70 (MQ=255)
                                                                    |                                                                  
AGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGAGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAA  >  AP009048/3824444‑3824577

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: