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 2,658,057 A→G 79.0% N342N (AAT→AAC) ‡ glpD ← sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,658,0570AG79.0% 143.7 / 26.2 99N342N (AAT→AAC) ‡glpDsn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding
Reads supporting (aligned to +/- strand):  ref base A (7/14);  new base G (63/15);  total (70/29)
Fisher's exact test for biased strand distribution p-value = 6.45e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

CCAGTTTTCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCACGGGTAATAGCCTGCGGCGAGTCGGA  >  minE/2657999‑2658113
                                                          |                                                        
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:2659389/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:213020/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:2001615/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:666449/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:910794/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:1036464/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:1671938/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:926592/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:155099/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:2696582/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:950092/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:3394685/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:3166099/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatc                                                  <  1:1102470/67‑1 (MQ=255)
ccAGTTTGCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcata                                                  <  1:3175879/67‑2 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:472405/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:3298389/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:3296675/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:2159419/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:1964135/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:2222807/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:1918154/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:574463/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:418610/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:1746640/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:1711020/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:1133574/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:2510806/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:1140679/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:2604240/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:1544486/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:1378793/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:1368968/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAg                                      >  1:2494585/1‑68 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAg                                      >  1:1835109/1‑68 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAg                                      >  1:1586498/1‑68 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAg                                      >  1:2163285/1‑68 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAg                                      >  1:3026484/1‑68 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGCGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:379614/1‑69 (MQ=255)
           tAGGTGGTCAGCTTACCGCCGAATACCGACAGAAGCGGGGCTTTGCCGTCTTCATCATGGATATCAAgg                                     >  1:1125351/1‑69 (MQ=255)
                ggtCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatca                                                 >  1:1078094/1‑52 (MQ=255)
                ggtCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatca                                                 >  1:1949790/1‑52 (MQ=255)
                ggtCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatca                                                 >  1:1172800/1‑52 (MQ=255)
                ggtCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatca                                                 >  1:3115191/1‑52 (MQ=255)
                ggtCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatca                                                 >  1:526664/1‑52 (MQ=255)
                ggtCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatca                                                 >  1:2366610/1‑52 (MQ=255)
                ggtCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatca                                                 >  1:3255440/1‑52 (MQ=255)
                ggtCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatca                                                 >  1:972509/1‑52 (MQ=255)
                ggtCAGCTTACCGCCGAATACCGACAGCAGCGGGGCTTTGCCGTCTtcatca                                                 >  1:2502202/1‑52 (MQ=255)
                    aGCTTACCGCCGAATACCGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCa                            >  1:1990251/1‑69 (MQ=255)
                    aGCTTACCGCCGAATACCGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCa                            >  1:2868041/1‑69 (MQ=255)
                    aGCTTACCGCCGAATACCGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCa                            >  1:1602928/1‑69 (MQ=255)
                    aGCTTACCGCCGAATACCGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCa                            >  1:2309934/1‑69 (MQ=255)
                    aGCTTACCGCCGAATACCGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCa                            >  1:2291871/1‑69 (MQ=255)
                    aGCTTACCGCCGAATACCGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCa                            >  1:10945/1‑69 (MQ=255)
                    aGCTTACCGCCGAATACCGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCa                            >  1:631652/1‑69 (MQ=255)
                           cgccgAATACCGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCACGGGTa                      <  1:1663540/68‑1 (MQ=255)
                            gccgAATACCGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCACGGGt                       <  1:3268716/66‑1 (MQ=255)
                            gccgAATACCGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCACGGGt                       <  1:1274967/66‑1 (MQ=255)
                              cgAATACCGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCACGGGt                       <  1:929657/64‑1 (MQ=255)
                                    ccGACAGCAGCGGTGCTTTGCCATTTTCATCATGaa                                             <  1:3143836/36‑1 (MQ=255)
                                    ccGACAGCAGCGGTGCTTTGCCATTTTCATCATGaa                                             <  1:2215339/36‑1 (MQ=255)
                                    ccGACAGCAGCGGTGCTTTGCCATTTTCATCATGaa                                             <  1:3220888/36‑1 (MQ=255)
                                    ccGACAGCAGCGGTGCTTTGCCATTTTCATCATGaa                                             <  1:3211458/36‑1 (MQ=255)
                                    ccGACAGCAGCGGTGCTTTGCCATTTTCATCATGaa                                             <  1:1756391/36‑1 (MQ=255)
                                    ccGACAGCAGCGGTGCTTTGCCATTTTCATCATGaa                                             <  1:3058041/36‑1 (MQ=255)
                                    ccGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGgtgt                                 <  1:509160/48‑1 (MQ=255)
                                    ccGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGgtgt                                 <  1:2744054/48‑1 (MQ=255)
                                    ccGACAGCAGCGGCGCTTTGCCATTTTCATCATGaa                                             <  1:559615/36‑1 (MQ=255)
                                            agcGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCACGGGTAATAGCCTGCGGCGAGTCg    <  1:433878/69‑1 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCa                            >  1:1723387/1‑43 (MQ=25)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTgt             >  1:1158781/1‑57 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCgg   >  1:3086649/1‑68 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCgg   >  1:2898413/1‑68 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:246470/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:981129/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:712910/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:716331/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:931341/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:3177265/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:104392/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:1152755/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:1210638/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:1497842/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:1610506/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:1654184/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:1760693/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:1804768/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:216011/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:2335860/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:2399044/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:2590577/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:2605104/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:277672/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:2943471/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:3411369/1‑69 (MQ=255)
                                              cGGGGCTTTGCCGTCTTCATCATCGATATCAAGGGTGTAATCACGGGTAATGGCCTg              >  1:1996023/1‑57 (MQ=25)
                                              cGGGGCTTCGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:1965271/1‑69 (MQ=255)
                                              cGGGGCATTGCCGTCTTCATCATGGATATCAAGGGTGTAATCACGGGTAATGGCCTGTGGCGAGTCGGa  >  1:442724/1‑69 (MQ=255)
                                                          |                                                        
CCAGTTTTCGGTAGGTGGTCAGCTTACCGCCGAATACCGACAGCAGCGGTGCTTTGCCATTTTCATCATGAATATCAAGGGTGTAATCACGGGTAATAGCCTGCGGCGAGTCGGA  >  minE/2657999‑2658113

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