Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A5 F1 I0 R2 201 99.6 7939938 96.9% 7693799 60.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,824,380 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
*W3110S.gb3,824,3800GA100.0% 348.5 / NA 116pseudogene (513/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (51/65);  total (51/65)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
*W3110S.gb3,824,3810GA100.0% 346.3 / NA 116pseudogene (514/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (51/65);  total (51/65)
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 116 total aligned reads displayed.

TGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCG  >  W3110S.gb/3824316‑3824444
                                                                ||                                                               
tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg                                                             >  1:283204/1‑70 (MQ=255)
  aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc                                                            <  1:7254816/69‑1 (MQ=255)
  aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc                                                            <  1:6098001/69‑1 (MQ=255)
  aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                           >  1:5650125/1‑70 (MQ=255)
  aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                                           >  1:604213/1‑70 (MQ=255)
  aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                          >  1:2190134/1‑71 (MQ=255)
  aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                          >  1:1628997/1‑71 (MQ=255)
   aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCTAt                                                         <  1:497281/71‑1 (MQ=255)
   aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                         >  1:4029612/1‑71 (MQ=255)
   aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                         >  1:6214607/1‑71 (MQ=255)
   aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                         <  1:1508906/71‑1 (MQ=255)
   aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                                         >  1:7566278/1‑71 (MQ=255)
    aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                                        >  1:6473557/1‑71 (MQ=255)
    aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                                        <  1:1446023/71‑1 (MQ=255)
    aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                                        >  1:4882689/1‑71 (MQ=255)
      ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg                                                      >  1:5948571/1‑71 (MQ=255)
       cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     <  1:253669/71‑1 (MQ=255)
       cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     <  1:2465982/71‑1 (MQ=255)
       cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     <  1:4420449/71‑1 (MQ=255)
       cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     <  1:827168/71‑1 (MQ=255)
       cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg                                                      >  1:341934/1‑70 (MQ=255)
        aacccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     >  1:4625934/4‑70 (MQ=255)
        aacccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     >  1:6657900/4‑70 (MQ=255)
        aacccGATGAAAGGGATGGTAGCC‑CAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                                   <  1:301614/68‑1 (MQ=255)
          cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                                   >  1:6965927/2‑70 (MQ=255)
             gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg                                               <  1:1402161/71‑1 (MQ=255)
               tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg                                                      >  1:2157606/1‑62 (MQ=255)
               tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                             >  1:3134025/1‑71 (MQ=255)
                gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                             >  1:2293782/1‑70 (MQ=255)
                gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                             >  1:2048639/1‑70 (MQ=255)
                 aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     <  1:5964785/61‑1 (MQ=255)
                 aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                            <  1:2334746/70‑1 (MQ=255)
                    gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGa                                        >  1:7381837/1‑71 (MQ=255)
                       aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActc                                     <  1:4917891/71‑1 (MQ=255)
                       aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                                      >  1:1821293/1‑70 (MQ=255)
                        tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                                          >  1:4007349/1‑49 (MQ=25)
                        tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                                      >  1:5108375/1‑69 (MQ=255)
                        tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                                      >  1:2246464/1‑69 (MQ=255)
                         ggTAGCCGCAGTTTCTGTCGGTATTGGAAACGGTGAAGCAATTTGCGAt                                                         <  1:7869876/49‑1 (MQ=19)
                          gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActcag                                   <  1:2034988/70‑3 (MQ=255)
                             gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                                            >  1:732421/1‑58 (MQ=255)
                               cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg                                >  1:3025637/1‑68 (MQ=255)
                                gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                          <  1:2779687/57‑1 (MQ=255)
                                gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                                          <  1:7256803/57‑1 (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                           <  1:4794930/71‑1 (MQ=255)
                                 cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                           <  1:5058258/71‑1 (MQ=255)
                                 cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag                           <  1:4233017/71‑1 (MQ=255)
                                  aGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga                          >  1:2589623/1‑71 (MQ=255)
                                   gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                         >  1:1883730/1‑71 (MQ=255)
                                   gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                         >  1:5687211/1‑71 (MQ=255)
                                   gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                         >  1:7425069/1‑71 (MQ=255)
                                    tttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                                             <  1:7923936/50‑1 (MQ=255)
                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     >  1:1024869/1‑40 (MQ=16)
                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     >  1:7438114/1‑40 (MQ=16)
                                      tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc                         >  1:2439976/1‑68 (MQ=255)
                                          tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     <  1:1621561/36‑1 (MQ=12)
                                          tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     <  1:2514973/36‑1 (MQ=12)
                                          tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                                     <  1:2615448/36‑1 (MQ=12)
                                          tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACAt                   >  1:6175232/1‑70 (MQ=255)
                                          tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg                  <  1:1680565/71‑1 (MQ=255)
                                          tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg                  <  1:1671366/71‑1 (MQ=255)
                                          tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACC‑ACATg                  <  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)
                                                ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                                      <  1:3002219/45‑1 (MQ=25)
                                                ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa            <  1:3721873/71‑1 (MQ=255)
                                                 tgtaAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                                      <  1:7823336/44‑1 (MQ=25)
                                                 tgtaAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct                                      <  1:4321038/44‑1 (MQ=25)
                                                  gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAg           <  1:7020579/67‑1 (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)
                                                    aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg         <  1:2235361/69‑1 (MQ=255)
                                                     aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCag                             >  1:5588589/1‑49 (MQ=37)
                                                     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   <  1:1311965/69‑1 (MQ=255)
                                                          tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg  <  1:2323506/70‑1 (MQ=255)
                                                          tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg  <  1:4092079/70‑1 (MQ=255)
                                                          tgAAGCAATTTGCGATCTGGAATACGTTAAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg  <  1:5467148/70‑1 (MQ=255)
                                                           gAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa                              <  1:6494900/42‑1 (MQ=37)
                                                           gAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAcc   >  1:2273193/1‑69 (MQ=255)
                                                           gAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg  >  1:5830675/1‑70 (MQ=255)
                                                           gAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg  >  1:3519890/1‑70 (MQ=255)
                                                                ||                                                               
TGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCG  >  W3110S.gb/3824316‑3824444

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: ‑

GATK/CNVnator alignment

N/A