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 3,824,362 A→T 100% pseudogene (495/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,3620AT97.0% 375.2 / 4.3 135pseudogene (495/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (67/64);  minor base G (4/0);  total (71/64)
Fisher's exact test for biased strand distribution p-value = 1.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01
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 135 total aligned reads displayed.

AAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATG  >  W3110S.gb/3824294‑3824428
                                                                    |                                                                  
aaGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                                  <  1:91027/71‑1 (MQ=255)
  gCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTATCCGCAGTTTCTGTCGGTATtg                                                                <  1:7046264/71‑1 (MQ=255)
  gCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAtt                                                                 >  1:6680186/1‑70 (MQ=255)
  gCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                                  >  1:3558915/1‑69 (MQ=255)
   cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgt                                                               <  1:4074926/71‑1 (MQ=255)
       tggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtg                                                                <  1:1427274/66‑1 (MQ=255)
         gAAAACGGCAAGCTGAAAACTAATCCAATGAAAGGGATGGTAGCCGCGGTCTCTGTCGGGATTGTGAAc                                                           >  1:274589/1‑69 (MQ=255)
         gAAAACGGCAAGCTGAAAACTAATCCAATGAAAGGGATGGTAGCCGCGGTCTCTGTCGGGATTGTGAAc                                                           >  1:5274513/1‑69 (MQ=255)
         gAAAACGGCAAGCTGAAAACTAATCCAATGAAAGGGATGGTAGCCGCGGTCTCTGTCGGGATTGTGAAc                                                           >  1:5645881/1‑69 (MQ=255)
         gAAAACGGCAAGCTGAAAACTAATCCAATGAAAGGGATGGTAGCCGCGGTCTCTGTCGGGATTGTGAAc                                                           >  1:1647026/1‑69 (MQ=255)
         gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                                                              >  1:6439135/1‑65 (MQ=255)
         gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                                                         <  1:5017540/71‑1 (MQ=255)
         gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                                                         <  1:5008591/71‑1 (MQ=255)
         gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                                                         >  1:3161862/1‑71 (MQ=255)
         gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg                                                          <  1:5065569/70‑1 (MQ=255)
         gAAAACCGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                                                         >  1:7692046/1‑71 (MQ=255)
           aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                       <  1:6904795/71‑3 (MQ=255)
           aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                       <  1:290001/71‑3 (MQ=255)
            aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGa                                                      <  1:6023278/71‑1 (MQ=255)
             aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                       >  1:7087252/1‑67 (MQ=255)
              cGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAg                                                    >  1:2094442/1‑71 (MQ=255)
              cGGAAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa                                                            >  1:1198378/1‑63 (MQ=255)
               ggCAAGCTGAAAACCTACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                                  <  1:4765612/56‑1 (MQ=255)
               ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt                                                                  <  1:204330/56‑1 (MQ=255)
                gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca                                                  <  1:5139121/71‑2 (MQ=255)
                 cAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                                                              <  1:4325445/58‑2 (MQ=255)
                 cAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaa                                                 >  1:7317590/1‑69 (MQ=255)
                    gCTGAAAACCAACACGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                                                              <  1:5557992/55‑2 (MQ=255)
                      tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                       >  1:5880210/1‑58 (MQ=255)
                      tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt                                                        <  1:3551120/59‑2 (MQ=255)
                       gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                       >  1:6074585/1‑57 (MQ=255)
                       gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                       >  1:456254/1‑57 (MQ=255)
                       gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                       >  1:3933074/1‑57 (MQ=255)
                        aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc                                            <  1:7254816/69‑1 (MQ=255)
                        aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc                                            <  1:6098001/69‑1 (MQ=255)
                        aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg                                           >  1:604213/1‑70 (MQ=255)
                        aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                          >  1:1628997/1‑71 (MQ=255)
                        aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa                                          >  1:2190134/1‑71 (MQ=255)
                         aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCTAt                                         <  1:497281/71‑1 (MQ=255)
                         aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                         <  1:1508906/71‑1 (MQ=255)
                         aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt                                         >  1:7566278/1‑71 (MQ=255)
                          aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg                                                          >  1:2853985/1‑53 (MQ=255)
                          aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                        >  1:4882689/1‑71 (MQ=255)
                          aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                        <  1:1446023/71‑1 (MQ=255)
                          aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc                                        >  1:6473557/1‑71 (MQ=255)
                             cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                     <  1:2465982/71‑1 (MQ=255)
                             cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                     <  1:827168/71‑1 (MQ=255)
                             cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                     <  1:4420449/71‑1 (MQ=255)
                             cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg                                      >  1:341934/1‑70 (MQ=255)
                              aacccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                     >  1:6657900/4‑70 (MQ=255)
                              aacccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                     >  1:4625934/4‑70 (MQ=255)
                              aacccGATGAAAGGGATGGTAGCC‑CAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                   <  1:301614/68‑1 (MQ=255)
                                cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                   >  1:4200866/2‑70 (MQ=255)
                                cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                   >  1:3580140/2‑70 (MQ=255)
                                cccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa                                   >  1:6965927/2‑70 (MQ=255)
                                  cGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgtaa                                                             >  1:5479122/1‑40 (MQ=38)
                                  cGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATAc                                <  1:6594128/71‑1 (MQ=255)
                                   gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa                                                            >  1:431653/1‑42 (MQ=38)
                                   gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa                                                            >  1:3171418/1‑42 (MQ=38)
                                    aTGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa                                                     >  1:2651908/1‑48 (MQ=255)
                                    aTGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa                                                     >  1:1272894/1‑48 (MQ=255)
                                     tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg                                      >  1:2157606/1‑62 (MQ=255)
                                     tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                             >  1:3134025/1‑71 (MQ=255)
                                      gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                                                       <  1:7304618/44‑3 (MQ=38)
                                      gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt                             >  1:2293782/1‑70 (MQ=255)
                                       aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt                                                        <  1:1684897/42‑2 (MQ=38)
                                       aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                     <  1:5964785/61‑1 (MQ=255)
                                       aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                            <  1:2334746/70‑1 (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)
                                               ggTAGCCGCAGTTTCTGTCGGTATTGGAAACGGTGAAGCAATTTGCGAt                                         <  1:7869876/49‑1 (MQ=19)
                                                gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActcag                   <  1:2034988/70‑3 (MQ=255)
                                                 tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc                 <  1:2234533/71‑1 (MQ=255)
                                                   gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg                            >  1:732421/1‑58 (MQ=255)
                                                   gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGc               <  1:2720575/71‑1 (MQ=255)
                                                      gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                          <  1:2779687/57‑1 (MQ=255)
                                                      gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa                          <  1:2348016/57‑1 (MQ=255)
                                                      gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga            <  1:6906349/71‑1 (MQ=255)
                                                      gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga            <  1:7771109/71‑1 (MQ=255)
                                                      gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa              >  1:2225744/1‑69 (MQ=255)
                                                       cAGTTTCTGTCGGTATTGTAAACTGTGAAGCAATTTGCGATCTTTAATACGTTGAAGACTCAGCCGCagag           <  1:3740734/71‑1 (MQ=255)
                                                       cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag           <  1:5058258/71‑1 (MQ=255)
                                                       cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag           <  1:4233017/71‑1 (MQ=255)
                                                        aGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga          >  1:2589623/1‑71 (MQ=255)
                                                         gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGc               >  1:5667497/1‑65 (MQ=255)
                                                         gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc         >  1:5687211/1‑71 (MQ=255)
                                                         gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc         >  1:1883730/1‑71 (MQ=255)
                                                         gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc         >  1:7425069/1‑71 (MQ=255)
                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                     >  1:7438114/1‑40 (MQ=16)
                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                     >  1:1024869/1‑40 (MQ=16)
                                                            tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc         >  1:2439976/1‑68 (MQ=255)
                                                                tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                     <  1:1621561/36‑1 (MQ=12)
                                                                tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                     <  1:5082583/36‑1 (MQ=12)
                                                                tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                     <  1:2615448/36‑1 (MQ=12)
                                                                tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg                                     <  1:2514973/36‑1 (MQ=12)
                                                                tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACAt   >  1:6175232/1‑70 (MQ=255)
                                                                tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg  <  1:1680565/71‑1 (MQ=255)
                                                                tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACC‑ACATg  <  1:3435336/70‑1 (MQ=255)
                                                                    |                                                                  
AAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATG  >  W3110S.gb/3824294‑3824428

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