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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,418,505 A→G 22.0% T51T (ACT→ACC)  rffM ← UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,418,5050AG22.0% 151.1 / 34.9 113T51T (ACT→ACC) rffMUDP‑N‑acetyl‑D‑mannosaminuronic acid transferase
Reads supporting (aligned to +/- strand):  ref base A (39/49);  new base G (2/23);  total (41/72)
Fisher's exact test for biased strand distribution p-value = 7.34e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.07e-01

Only 100 of 115 total aligned reads displayed.

CCATCCGCATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAT  >  minE/2418443‑2418572
                                                              |                                                                   
ccATCCGCATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGc                                                               >  1:933894/1‑69 (MQ=255)
ccATCCGCATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGc                                                               >  1:663108/1‑69 (MQ=255)
       cATATTTAAATTCGTCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:2986579/68‑1 (MQ=255)
       cATATTTAAATTCGTCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:3005373/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAAGTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:567346/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:43349/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:3426823/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:926498/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:2246773/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:2284450/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:56586/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:2544717/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:2561353/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:2653229/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:1002172/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:2844879/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:96907/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:2988628/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:413997/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:3011884/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:3311586/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:1708929/68‑1 (MQ=255)
       cATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATGGTCAGCAttttt                                                         <  1:96766/68‑1 (MQ=255)
        atatTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTc                                                       <  1:1778917/69‑1 (MQ=255)
        atatTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTc                                                       <  1:646633/69‑1 (MQ=255)
        atatTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTc                                                       <  1:59127/69‑1 (MQ=255)
         tatTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTc                                                       <  1:3296931/68‑1 (MQ=255)
           tttAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGc                                                    >  1:2694618/1‑69 (MQ=255)
           tttAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGc                                                    >  1:2765758/1‑69 (MQ=255)
           tttAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGc                                                    >  1:490171/1‑69 (MQ=255)
           tttAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGc                                                    >  1:2491635/1‑69 (MQ=255)
           tttAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGc                                                    >  1:3101624/1‑69 (MQ=255)
           tttAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGc                                                    >  1:1395011/1‑69 (MQ=255)
           tttAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGc                                                    >  1:288325/1‑69 (MQ=255)
                     gCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGc                                           <  1:121269/68‑1 (MQ=255)
                     gCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGc                                           <  1:2841683/68‑1 (MQ=255)
                     gCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGc                                           <  1:2896349/68‑1 (MQ=255)
                     gCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGc                                           <  1:2975041/68‑1 (MQ=255)
                     gCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGc                                           <  1:1342060/68‑1 (MQ=255)
                     gCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGc                                           <  1:227515/68‑1 (MQ=255)
                      cAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          <  1:3319420/68‑1 (MQ=255)
                      cAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          <  1:2733181/68‑1 (MQ=255)
                      cAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          <  1:1181173/68‑1 (MQ=255)
                      cAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          <  1:1899119/68‑1 (MQ=255)
                      cAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          <  1:2191724/68‑1 (MQ=255)
                      cAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          <  1:2471198/68‑1 (MQ=255)
                           ttaattaaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCAtt                                                 <  1:1385670/56‑1 (MQ=255)
                           ttaattaaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCAtt                                                 <  1:1469917/56‑1 (MQ=255)
                           ttaattaaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCAtt                                                 <  1:1511542/56‑1 (MQ=255)
                           ttaattaaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCAtt                                                 <  1:1908096/56‑1 (MQ=255)
                           ttaattaaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCAtt                                                 <  1:522271/56‑1 (MQ=255)
                           ttaattaaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCAtt                                                 <  1:2040716/56‑1 (MQ=255)
                           ttaattaaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCAtt                                                 <  1:2388114/56‑1 (MQ=255)
                           ttaattaaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCAtt                                                 <  1:2785622/56‑1 (MQ=255)
                           ttaattaaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCAtt                                                 <  1:1418314/56‑1 (MQ=255)
                           ttaattaaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCAtt                                                 <  1:2148199/56‑1 (MQ=255)
                           ttaattaaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCAtt                                                 <  1:2879860/56‑1 (MQ=255)
                           ttaattaaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCAtt                                                 <  1:3320017/56‑1 (MQ=255)
                           ttaattaaCTCCCTGACCTCGGCGTTATCTTCAATAGACAGCATTTTTTCAGCAtt                                                 <  1:3123700/56‑1 (MQ=255)
                                 aaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTccc                              >  1:2628349/1‑69 (MQ=255)
                                 aaCTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTccc                              >  1:2482469/1‑69 (MQ=255)
                                    tCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          >  1:3426755/1‑54 (MQ=255)
                                    tCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          >  1:1691635/1‑54 (MQ=255)
                                    tCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          >  1:1130526/1‑54 (MQ=255)
                                    tCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          >  1:2637847/1‑54 (MQ=255)
                                    tCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          >  1:1565646/1‑54 (MQ=255)
                                    tCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          >  1:13899/1‑54 (MQ=255)
                                    tCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          >  1:2698136/1‑54 (MQ=255)
                                    tCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          >  1:1518319/1‑54 (MQ=255)
                                    tCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          >  1:2957471/1‑54 (MQ=255)
                                    tCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          >  1:154445/1‑54 (MQ=255)
                                    tCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          >  1:2869216/1‑54 (MQ=255)
                                    tCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCa                                          >  1:596280/1‑54 (MQ=255)
                                    tCCCTGACCTCGGCGTTATCTTCAATAGTCAGAATTTTTTCAGCATTAATGGCa                                          >  1:205888/1‑54 (MQ=255)
                                     cccTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGc                                           <  1:949367/52‑1 (MQ=255)
                                            cTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTg                   <  1:504886/69‑1 (MQ=255)
                                            cTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTg                   >  1:452390/1‑69 (MQ=255)
                                            cTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTg                   >  1:942750/1‑69 (MQ=255)
                                            cTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTg                   >  1:699633/1‑69 (MQ=255)
                                             tCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTg                   <  1:65078/68‑1 (MQ=255)
                                             tCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTg                   <  1:2286837/68‑1 (MQ=255)
                                                          cAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTa                        <  1:2738205/50‑1 (MQ=255)
                                                          cAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTa                        <  1:680236/50‑1 (MQ=255)
                                                          cAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTa                        <  1:144009/50‑1 (MQ=255)
                                                          cAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTa                        <  1:2627651/50‑1 (MQ=255)
                                                          cAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTa                        <  1:2527041/50‑1 (MQ=255)
                                                          cAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTa                        <  1:2470202/50‑1 (MQ=255)
                                                          cAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTa                        <  1:179929/50‑1 (MQ=255)
                                                             tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGa   <  1:3371381/68‑1 (MQ=255)
                                                             tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGa   <  1:2253291/68‑1 (MQ=255)
                                                             tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGa   <  1:2031578/68‑1 (MQ=255)
                                                             tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt  >  1:1119612/1‑69 (MQ=255)
                                                             tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt  >  1:474920/1‑69 (MQ=255)
                                                             tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt  >  1:1137657/1‑69 (MQ=255)
                                                             tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt  >  1:1252000/1‑69 (MQ=255)
                                                             tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt  >  1:2387966/1‑69 (MQ=255)
                                                             tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt  >  1:2755616/1‑69 (MQ=255)
                                                             tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt  >  1:564525/1‑69 (MQ=255)
                                                              aGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGa   <  1:3180696/67‑1 (MQ=255)
                                                              aGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGa   <  1:431656/67‑1 (MQ=255)
                                                              |                                                                   
CCATCCGCATATTTAAATTCGGCAGCGTTAATTAACTCCCTGACCTCGGCGTTATCTTCAATAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAT  >  minE/2418443‑2418572

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: ‑

GATK/CNVnator alignment

N/A