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 1,294,414 C→T 35.5% S277S (TCG→TCA)  nac ← DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,294,4140CT35.5% 61.8 / 49.9 87S277S (TCG→TCA) nacDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base C (21/35);  new base T (16/15);  total (37/50)
Fisher's exact test for biased strand distribution p-value = 2.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.34e-01

TGCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGT  >  minE/1294346‑1294480
                                                                    |                                                                  
tGCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGc                                                                    >  1:2233730/1‑69 (MQ=255)
tGCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGc                                                                    >  1:2177637/1‑69 (MQ=255)
tGCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGc                                                                    >  1:208972/1‑69 (MQ=255)
tGCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGc                                                                    >  1:1829144/1‑69 (MQ=255)
tGCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGc                                                                    >  1:1731358/1‑69 (MQ=255)
tGCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGc                                                                    >  1:1631097/1‑69 (MQ=255)
tGCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGc                                                                    >  1:1461895/1‑69 (MQ=255)
 gCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGc                                                                    >  1:1008491/1‑68 (MQ=255)
 gCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGc                                                                    >  1:2714577/1‑68 (MQ=255)
 gCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGc                                                                    >  1:2874399/1‑68 (MQ=255)
 gCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGc                                                                    >  1:2985430/1‑68 (MQ=255)
 gCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGc                                                                    >  1:3430124/1‑68 (MQ=255)
 gCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACAGCCTGTGCCTGTGGc                                                                    >  1:1442317/1‑68 (MQ=255)
    ttttttCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGAt                                                                 <  1:260809/68‑1 (MQ=255)
    ttttttCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGAt                                                                 <  1:2138076/68‑1 (MQ=255)
               aCTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTg                                                     >  1:471948/1‑69 (MQ=255)
               aCTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTg                                                     >  1:1374557/1‑69 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCg                                                  >  1:582460/1‑61 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCg                                                  >  1:1345410/1‑61 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTaaa                                            >  1:143635/1‑67 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTaaa                                            >  1:3240263/1‑67 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTaaa                                            >  1:1985688/1‑67 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTaaa                                            >  1:1887239/1‑67 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                           >  1:1749897/1‑68 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                           >  1:2576803/1‑68 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                           >  1:1056387/1‑68 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                           >  1:2362576/1‑68 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                           >  1:3383063/1‑68 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                           >  1:3401758/1‑68 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                           >  1:1359146/1‑68 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                           >  1:765992/1‑68 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                           >  1:2200556/1‑68 (MQ=255)
                          aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                           >  1:1141716/1‑68 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:470355/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:2618313/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:2557345/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:1614331/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:844807/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:350005/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:643392/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:2006242/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:2002352/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:1983008/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:427821/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:1831097/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:403133/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:372293/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAAttt                                         <  1:3297362/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAAttt                                         <  1:450242/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAAttt                                         <  1:94592/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAAttt                                         <  1:1021220/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAAttt                                         <  1:1662947/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGAGGGTAAAttt                                         <  1:2506822/67‑1 (MQ=255)
                             cACTGACATTAACAACTCTTTCACTGCCAGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAAttt                                         <  1:1141574/67‑1 (MQ=255)
                              aCTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAAt                                      >  1:2286988/1‑69 (MQ=255)
                              aCTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAAt                                      >  1:3407443/1‑69 (MQ=255)
                              aCTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAAt                                      >  1:2229725/1‑69 (MQ=255)
                                tGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                         <  1:1301192/64‑1 (MQ=255)
                                    aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                <  1:748245/69‑1 (MQ=255)
                                    aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                <  1:3376550/69‑1 (MQ=255)
                                    aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                <  1:371605/69‑1 (MQ=255)
                                    aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                <  1:795354/69‑1 (MQ=255)
                                    aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                <  1:844453/69‑1 (MQ=255)
                                    aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACa                                  <  1:2574273/67‑1 (MQ=255)
                                    aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCCGGTAAATTTAATGACaaa                                <  1:2236309/69‑1 (MQ=255)
                                      tAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAaga                              <  1:1108862/69‑1 (MQ=255)
                                       aacaacTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                >  1:1751982/1‑66 (MQ=255)
                                       aacaacTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                >  1:755710/1‑66 (MQ=255)
                                       aacaacTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                >  1:3302679/1‑66 (MQ=255)
                                       aacaacTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                >  1:2384591/1‑66 (MQ=255)
                                                ttCACTGCCTGTGCCTGTGGCGATAAGTTCGctct                                                      >  1:2425734/1‑35 (MQ=255)
                                                ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                     >  1:1377795/1‑68 (MQ=255)
                                                ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                     >  1:2976663/1‑68 (MQ=255)
                                                ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                     >  1:649082/1‑68 (MQ=255)
                                                ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                     >  1:3182513/1‑68 (MQ=255)
                                                ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                     >  1:860750/1‑68 (MQ=255)
                                                ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                     >  1:32009/1‑68 (MQ=255)
                                                ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                     >  1:2587328/1‑68 (MQ=255)
                                                ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                     >  1:2110337/1‑68 (MQ=255)
                                                ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                     >  1:2832004/1‑68 (MQ=255)
                                                     tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACt                        <  1:3338923/60‑1 (MQ=255)
                                                     tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg               <  1:1726422/69‑1 (MQ=255)
                                                     tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg               <  1:1655149/69‑1 (MQ=255)
                                                     tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg               <  1:1480796/69‑1 (MQ=255)
                                                     tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg               <  1:490750/69‑1 (MQ=255)
                                                     tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg               <  1:873604/69‑1 (MQ=255)
                                                     tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg               <  1:2845626/69‑1 (MQ=255)
                                                     tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg               <  1:837029/69‑1 (MQ=255)
                                                     tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg               <  1:1141889/69‑1 (MQ=255)
                                                     tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg               <  1:782788/69‑1 (MQ=255)
                                                     tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg               <  1:2934565/69‑1 (MQ=255)
                                                      gcctgtgcctgtGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg               <  1:965572/68‑1 (MQ=255)
                                                             cctgtgGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAaga                              <  1:586339/46‑1 (MQ=255)
                                                             cctgtgGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAaga                              <  1:583241/46‑1 (MQ=255)
                                                             cctgtgGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAaga                              <  1:873590/46‑1 (MQ=255)
                                                             cctgtgGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAaga                              <  1:3408701/46‑1 (MQ=255)
                                                             cctgtgGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGt         <  1:3282400/67‑1 (MQ=255)
                                                                   gCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGt         >  1:3127008/1‑61 (MQ=255)
                                                                   gCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGt         >  1:2555794/1‑61 (MQ=255)
                                                                   gCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGt  <  1:1328243/68‑1 (MQ=255)
                                                                    |                                                                  
TGCCTTTTTTCCATCACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGT  >  minE/1294346‑1294480

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A