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 1,294,444 T→G 47.7% S267S (TCA→TCC)  nac ← DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,294,4440TG47.7% 0.3 / 152.2 130S267S (TCA→TCC) nacDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base T (41/27);  new base G (21/41);  total (62/68)
Fisher's exact test for biased strand distribution p-value = 2.97e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 133 total aligned reads displayed.

ACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATA  >  minE/1294376‑1294508
                                                                    |                                                                
aCTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAAt                                                                  >  1:2286988/1‑69 (MQ=255)
aCTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAAt                                                                  >  1:2229725/1‑69 (MQ=255)
      aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                                            <  1:3376550/69‑1 (MQ=255)
      aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                                            <  1:371605/69‑1 (MQ=255)
      aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                                            <  1:844453/69‑1 (MQ=255)
         aacaacTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                                            >  1:3302679/1‑66 (MQ=255)
         aacaacTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                                            >  1:755710/1‑66 (MQ=255)
                  ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                                                 >  1:2587328/1‑68 (MQ=255)
                  ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                                                 >  1:2110337/1‑68 (MQ=255)
                  ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                                                 >  1:3182513/1‑68 (MQ=255)
                  ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                                                 >  1:649082/1‑68 (MQ=255)
                  ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                                                 >  1:2976663/1‑68 (MQ=255)
                  ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                                                 >  1:1377795/1‑68 (MQ=255)
                  ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                                                 >  1:2832004/1‑68 (MQ=255)
                       tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                           <  1:782788/69‑1 (MQ=255)
                       tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                           <  1:837029/69‑1 (MQ=255)
                       tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                           <  1:1480796/69‑1 (MQ=255)
                       tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                           <  1:873604/69‑1 (MQ=255)
                       tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                           <  1:1141889/69‑1 (MQ=255)
                       tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                           <  1:1655149/69‑1 (MQ=255)
                       tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                           <  1:2934565/69‑1 (MQ=255)
                       tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                           <  1:1726422/69‑1 (MQ=255)
                               cctgtgGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAaga                                                          <  1:873590/46‑1 (MQ=255)
                               cctgtgGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAaga                                                          <  1:583241/46‑1 (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)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAGGAGAGACTc                                                   <  1:2074598/42‑1 (MQ=25)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                                                   <  1:1693176/42‑1 (MQ=37)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                                                   <  1:3425525/42‑1 (MQ=37)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                                                   <  1:386658/42‑1 (MQ=37)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                                                   <  1:2483998/42‑1 (MQ=37)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                                                   <  1:2422919/42‑1 (MQ=37)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                                                   <  1:2971157/42‑1 (MQ=37)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                                                   <  1:940553/42‑1 (MQ=37)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                                                   <  1:2949382/42‑1 (MQ=37)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                                                   <  1:2910214/42‑1 (MQ=37)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                                                   <  1:1079292/42‑1 (MQ=37)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAAt                                  >  1:883800/3‑61 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGAc                           >  1:110306/3‑68 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:1068813/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:2558939/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:92250/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:764479/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:3027479/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:47985/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:377712/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:1251145/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:1520693/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:1707178/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:2380009/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:1780949/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:1866301/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:2282731/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:2291214/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGAGGTAATGCGTGACa                          >  1:3345797/3‑69 (MQ=255)
                                        acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTAATTGAAGGAGTGGTAATGCGTGACa                          >  1:47611/3‑69 (MQ=255)
                                        acaaGTTTGATCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa                          >  1:1473342/3‑69 (MQ=255)
                                         caaGTTTGCTCTGGCGTGTAAATTTAAGGACAAAGAGAGACTc                                                   <  1:1066452/42‑1 (MQ=255)
                                          aaGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATc                        >  1:1618141/1‑69 (MQ=255)
                                          aaGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATc                        >  1:2136766/1‑69 (MQ=255)
                                          aaGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATc                        >  1:1248245/1‑69 (MQ=255)
                                          aaGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATc                        >  1:3286672/1‑69 (MQ=255)
                                            gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTaa                                   >  1:1253904/1‑56 (MQ=255)
                                            gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACa                          >  1:823143/1‑65 (MQ=255)
                                            gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                      >  1:2942254/1‑69 (MQ=255)
                                            gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                      >  1:572479/1‑69 (MQ=255)
                                            gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                      >  1:2886081/1‑69 (MQ=255)
                                            gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                      >  1:1896914/1‑69 (MQ=255)
                                            gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                      >  1:921735/1‑69 (MQ=255)
                                             ttCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa                      >  1:1636824/1‑68 (MQ=255)
                                              tCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                                           <  1:2741625/46‑1 (MQ=255)
                                                          gTAAATTTAAGGACAAAGAGAGACTCAT‑TAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:296263/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:1200065/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:1421030/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:1433109/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:11547/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:675859/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:1516643/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:590118/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:2392564/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:3389385/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:2194923/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:2170328/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:3108918/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:2146718/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:2346250/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:2822231/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:376162/69‑1 (MQ=255)
                                                           tAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:2772046/69‑1 (MQ=255)
                                                              aTTTAAGGACAAAGAGAGAGTCATTGAAGGAGTTGTAATGCGTGACATCCACCCATTTACTGCGcc       <  1:2080230/66‑1 (MQ=255)
                                                                ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTAc             >  1:2387542/1‑58 (MQ=255)
                                                                ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACAt   >  1:260034/1‑68 (MQ=255)
                                                                ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACAt   >  1:471581/1‑68 (MQ=255)
                                                                ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATa  >  1:1497334/1‑69 (MQ=255)
                                                                ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATa  >  1:1820371/1‑69 (MQ=255)
                                                                ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATa  >  1:536392/1‑69 (MQ=255)
                                                                ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATa  >  1:2327394/1‑69 (MQ=255)
                                                                ttAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATa  >  1:1528204/1‑69 (MQ=255)
                                                                    |                                                                
ACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCACCCATTTACTGCGCCACATA  >  minE/1294376‑1294508

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