Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,824,374 C→T 100% pseudogene (507/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,3740CT100.0% 272.0 / NA 93pseudogene (507/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (51/42);  total (51/42)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGA  >  W3110S.gb/3824310‑3824441
                                                                |                                                                   
gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGc                                                                >  1:3943012/1‑70 (MQ=255)
      tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc                                                         >  1:610660/1‑71 (MQ=255)
        aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                        <  1:3496848/70‑1 (MQ=255)
        aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                        <  1:350950/70‑1 (MQ=255)
           aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                        <  1:3361217/67‑1 (MQ=255)
             cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  <  1:1021298/71‑1 (MQ=255)
             cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  <  1:2033232/71‑1 (MQ=255)
             cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGGCGGTATTGTAACCGGTGAAGCAATTTGCGATCTgg                                                  <  1:3730322/71‑1 (MQ=255)
             cAACCCGATGAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  <  1:1766045/70‑1 (MQ=255)
               acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                                <  1:606789/69‑1 (MQ=255)
                cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                        <  1:3612276/61‑1 (MQ=255)
                 ccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                       >  1:211847/1‑62 (MQ=255)
                 ccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                      >  1:2002473/1‑63 (MQ=255)
                 ccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                      >  1:2570181/1‑63 (MQ=255)
                 ccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                      >  1:1648232/1‑63 (MQ=255)
                     tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa                                              <  1:2110420/67‑1 (MQ=255)
                     tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATa                                              <  1:4010269/67‑1 (MQ=255)
                     tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGCAATa                                              <  1:1312683/67‑1 (MQ=255)
                      gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                          >  1:3640234/1‑70 (MQ=255)
                        aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                       <  1:695342/71‑1 (MQ=255)
                          gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                                >  1:2627856/1‑60 (MQ=255)
                          gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGa                                     >  1:3939322/1‑71 (MQ=255)
                             aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                  <  1:2792880/55‑1 (MQ=255)
                              tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca                                                               <  1:2212050/41‑2 (MQ=37)
                              tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca                                                               <  1:2779632/41‑2 (MQ=37)
                              tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca                                                               <  1:3073153/41‑2 (MQ=37)
                              tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca                                                               <  1:3927718/41‑2 (MQ=37)
                              tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca                                                               <  1:1062499/41‑2 (MQ=37)
                              tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca                                                               <  1:3548620/41‑2 (MQ=37)
                              tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca                                                               <  1:93076/41‑2 (MQ=37)
                                gTAGCCTCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                       <  1:550/63‑1 (MQ=255)
                                gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                        <  1:2418701/46‑1 (MQ=25)
                                gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                       >  1:3494366/1‑63 (MQ=255)
                                gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                       >  1:4070183/1‑63 (MQ=255)
                                gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                       >  1:3337982/1‑63 (MQ=255)
                                gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                       >  1:681364/1‑63 (MQ=255)
                                gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc                               >  1:2409979/1‑71 (MQ=255)
                                 tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                       >  1:841309/1‑46 (MQ=25)
                                 tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                       >  1:1723619/1‑46 (MQ=25)
                                 tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                       >  1:1793118/1‑46 (MQ=25)
                                 tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc                              >  1:3556558/1‑71 (MQ=255)
                                 tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc                              >  1:3234946/1‑71 (MQ=255)
                                   gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg                             <  1:363868/70‑1 (MQ=255)
                                    ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                           <  1:3462913/71‑1 (MQ=255)
                                    ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                           <  1:3884274/71‑1 (MQ=255)
                                     cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg                             >  1:975391/1‑68 (MQ=255)
                                           ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc                     >  1:3221884/1‑70 (MQ=255)
                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGa                                                 >  1:3889590/1‑41 (MQ=19)
                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                   >  1:1003676/1‑71 (MQ=255)
                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                   >  1:3724334/1‑71 (MQ=255)
                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                   >  1:1253759/1‑71 (MQ=255)
                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                   >  1:107740/1‑71 (MQ=255)
                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                   >  1:806512/1‑71 (MQ=255)
                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                   >  1:2713519/1‑71 (MQ=255)
                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa                   >  1:2740603/1‑71 (MQ=255)
                                                  ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa             >  1:1427256/4‑71 (MQ=255)
                                                    taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                           <  1:625363/54‑1 (MQ=255)
                                                    taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                           <  1:3338627/54‑1 (MQ=255)
                                                      ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                          <  1:2484554/38‑1 (MQ=21)
                                                      ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                          <  1:2361327/38‑1 (MQ=21)
                                                      ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                          <  1:2071848/38‑1 (MQ=21)
                                                      ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                          <  1:1858261/38‑1 (MQ=21)
                                                      ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg           >  1:1263306/1‑69 (MQ=255)
                                                       tgtaAACGGTGAAGCAATTTGCGATCTGGAATTCGtt                                          <  1:3684138/37‑1 (MQ=12)
                                                       tgtaAACGGTCAAGCAATTTGCGATCTGGAATACGtt                                          <  1:602387/37‑1 (MQ=12)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGAc                  >  1:851383/4‑60 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:3151080/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:9525/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:908874/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:49176/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:489704/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:2265045/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:1016059/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:127790/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:1316820/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:1322062/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:1325536/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:1350753/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:1530920/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:2187513/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:3616225/4‑71 (MQ=255)
                                                        gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       >  1:3232911/4‑71 (MQ=255)
                                                         taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg      <  1:3213145/69‑1 (MQ=255)
                                                         taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       <  1:600399/68‑1 (MQ=255)
                                                         taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       <  1:1949343/68‑1 (MQ=255)
                                                         taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       <  1:2532040/68‑1 (MQ=255)
                                                         taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt       <  1:3391885/68‑1 (MQ=255)
                                                           aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat    >  1:2344563/1‑71 (MQ=255)
                                                           aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat    <  1:2500666/71‑1 (MQ=255)
                                                           aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat    <  1:600091/71‑1 (MQ=255)
                                                           aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat    >  1:2907660/1‑71 (MQ=255)
                                                            aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg   <  1:160252/71‑1 (MQ=255)
                                                             cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatga  >  1:2882294/1‑71 (MQ=255)
                                                                |                                                                   
GCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGA  >  W3110S.gb/3824310‑3824441

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: