Predicted mutation
evidence seq id position mutation freq annotation gene description
RA AP009048 3,824,522 T→G 100% pseudogene (657/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AP0090483,824,5220TG100.0% 222.7 / NA 63pseudogene (657/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (28/35);  total (28/35)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGAGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTA  >  AP009048/3824454‑3824587
                                                                    |                                                                  
atcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGcgct                                                                  <  1:1449623/71‑1 (MQ=255)
 tcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTg                                                                 >  1:1924400/1‑71 (MQ=255)
    ttGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGcc                                                              >  1:4428589/1‑71 (MQ=255)
     tGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGccc                                                             >  1:2506552/1‑71 (MQ=255)
      gAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGccc                                                             >  1:3990242/1‑70 (MQ=255)
       aaGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg                                                            <  1:3293658/70‑1 (MQ=255)
           gCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgggg                                                      >  1:4622212/1‑71 (MQ=255)
            cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgggg                                                      >  1:3305026/1‑70 (MQ=255)
            cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgggg                                                      <  1:3109300/70‑1 (MQ=255)
            cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgggg                                                      <  1:2631034/70‑1 (MQ=255)
            cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgggg                                                      <  1:1734948/70‑1 (MQ=255)
            cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgggg                                                      <  1:2559829/70‑1 (MQ=255)
               gggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGACCGAgggggaa                                                   >  1:3599581/1‑67 (MQ=255)
                 gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcg                                                 <  1:1557950/71‑1 (MQ=255)
                 gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAggg                                                       <  1:299834/64‑1 (MQ=255)
                  aCGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcga                                                <  1:3871590/71‑1 (MQ=255)
                   cGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgggg                                                      <  1:1807758/63‑1 (MQ=255)
                      cAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATcc                                            <  1:411236/71‑1 (MQ=255)
                       aGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCa                                           <  1:2246513/71‑1 (MQ=255)
                         aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAtt                                         >  1:1719010/1‑71 (MQ=255)
                         aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgggg                                                      >  1:2894228/1‑57 (MQ=255)
                          aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTg                                        <  1:4632748/71‑1 (MQ=255)
                              gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTg                                        <  1:4486315/67‑1 (MQ=255)
                              gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTa                                      >  1:4043597/1‑69 (MQ=255)
                                   gTTCACACATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACg                                >  1:668943/1‑70 (MQ=255)
                                      cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaat                                              >  1:163769/1‑53 (MQ=255)
                                      cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                             >  1:3640694/1‑70 (MQ=255)
                                        cccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAg                          >  1:176646/1‑71 (MQ=255)
                                          cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcg                                                 <  1:3332186/46‑1 (MQ=255)
                                          cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggc                        <  1:369018/71‑1 (MQ=255)
                                           aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaat                                              <  1:1469018/48‑1 (MQ=255)
                                           aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGc                               >  1:197602/1‑63 (MQ=255)
                                           aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcg                       <  1:1850322/71‑1 (MQ=255)
                                            tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAggggg                                                     >  1:2176843/1‑38 (MQ=37)
                                            tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAgggg                                                      <  1:5143487/38‑1 (MQ=38)
                                             gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaa                                               >  1:2672562/1‑45 (MQ=255)
                                              aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg                    <  1:2654322/71‑1 (MQ=255)
                                               agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGgcgc                   <  1:1267080/71‑1 (MQ=255)
                                                gagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                             <  1:3357141/60‑1 (MQ=255)
                                                 agCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa                           <  1:469377/61‑1 (MQ=255)
                                                 agCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTg                 >  1:4600752/1‑71 (MQ=255)
                                                  gCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTgg                >  1:2565127/1‑71 (MQ=255)
                                                  gCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTg                 <  1:1739820/70‑1 (MQ=255)
                                                   cTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGc                                    <  1:539001/50‑1 (MQ=255)
                                                      cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCaa             <  1:3375744/70‑1 (MQ=255)
                                                       tCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGa                                  >  1:2412801/1‑48 (MQ=255)
                                                        caccTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt          >  1:790400/4‑71 (MQ=255)
                                                         accTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGGAAACTg         <  1:10642/69‑1 (MQ=255)
                                                         accTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTg         <  1:2769712/69‑1 (MQ=255)
                                                         accTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTg         <  1:3509588/69‑1 (MQ=255)
                                                          ccTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGa        <  1:2986389/70‑1 (MQ=255)
                                                           cTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAt       <  1:780935/71‑1 (MQ=255)
                                                           cTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAt       <  1:31328/71‑1 (MQ=255)
                                                            ttgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGa                                  >  1:4222649/1‑43 (MQ=37)
                                                            ttgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt      >  1:439361/1‑71 (MQ=255)
                                                            ttgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt      >  1:5059793/1‑71 (MQ=255)
                                                             tgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt      >  1:4863042/1‑70 (MQ=255)
                                                             tgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt      >  1:1389476/1‑70 (MQ=255)
                                                              gttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtttt    >  1:4115959/1‑71 (MQ=255)
                                                               ttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                             <  1:948076/45‑1 (MQ=255)
                                                               ttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcgg                      >  1:4122365/1‑52 (MQ=255)
                                                                 ggCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa  <  1:532245/70‑1 (MQ=255)
                                                                 ggCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa  <  1:2264267/70‑1 (MQ=255)
                                                                 ggCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa  <  1:4133903/70‑1 (MQ=255)
                                                                    |                                                                  
ATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGAGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTA  >  AP009048/3824454‑3824587

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: