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 2,520,256 C→T 28.3% intergenic (‑210/‑48) gmk ← / → ligB guanylate kinase/DNA ligase, NAD(+)‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,520,2560CT28.3% 136.0 / 52.3 123intergenic (‑210/‑48)gmk/ligBguanylate kinase/DNA ligase, NAD(+)‑dependent
Reads supporting (aligned to +/- strand):  ref base C (52/36);  new base T (19/16);  total (71/52)
Fisher's exact test for biased strand distribution p-value = 6.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.94e-01

Only 100 of 133 total aligned reads displayed.

CATTCACTGCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAGTATGGATGGCGA  >  minE/2520188‑2520322
                                                                    |                                                                  
cATTCACTGCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGgctttgc                                                                    >  1:3973/1‑69 (MQ=255)
cATTCACTGCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGgctttgc                                                                    >  1:2570185/1‑69 (MQ=255)
cATTCACTGCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGgctttgc                                                                    >  1:1431968/1‑69 (MQ=255)
        gCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGGCACTCGGCTTTGCTTtcatca                                                            >  1:242356/1‑69 (MQ=255)
        gCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTtcatca                                                            >  1:2179996/1‑69 (MQ=255)
        gCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTtcatca                                                            >  1:2276665/1‑69 (MQ=255)
        gCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTtcatca                                                            >  1:1595863/1‑69 (MQ=255)
        gCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTtcatca                                                            >  1:320925/1‑69 (MQ=255)
        gCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTtcatca                                                            >  1:1398360/1‑69 (MQ=255)
        gCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTtcatca                                                            >  1:2115532/1‑69 (MQ=255)
        gCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTtcatc                                                             >  1:2897918/1‑68 (MQ=255)
        gCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGACACTCGGCTTTGCTTtcatca                                                            >  1:777268/1‑69 (MQ=255)
           aTAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCAc                                                           <  1:1710012/67‑1 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTtcat                                                              >  1:2489589/1‑61 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGtt                                                        >  1:520540/1‑67 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:1527747/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:359818/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:1862739/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:3429049/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:3078812/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:1653791/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:1978612/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:2043886/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:2300704/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:3311440/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:2195591/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:2196644/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:1131573/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:1120228/1‑68 (MQ=255)
              aaGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTg                                                       >  1:953313/1‑68 (MQ=255)
                              aGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCT‑CCTGACTATc                                     <  1:2356099/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTTCACCAAGTTGTATATCTGCCTGACTATc                                     <  1:2265857/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTTCACCAAGTTGTATATCTGCCTGACTATc                                     <  1:3133505/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTTCACCAAGTTGTATATCTGCCTGACTATc                                     <  1:3334413/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTTCACCAAGTTGTATATCTGCCTGACTATc                                     <  1:505554/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTTCACCAAGTTGTATATCTGCCTGACTATc                                     <  1:564427/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTTCACCAAGTTGTATATCTGCCTGACTATc                                     <  1:3024117/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTTCACCAAGTTGTATATCTGCCTGACTATc                                     <  1:749990/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTTCACCAAGTTGTATATCTGCCTGACTATc                                     <  1:1151890/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTTCACCAAGTTGTATATCTGCCTGACTATc                                     <  1:2682813/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATc                                     <  1:2750470/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATc                                     <  1:2632489/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATc                                     <  1:1716731/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATc                                     <  1:2260744/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATc                                     <  1:1461358/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATc                                     <  1:1005770/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATc                                     <  1:885281/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATc                                     <  1:1181429/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATc                                     <  1:1147808/69‑1 (MQ=255)
                               gCGTCCTCGCAGACTCCGTTTATGCCACTCGGCTTTGTCTTCACTAAGTTGTATATCTGCCTGACTATc                                     <  1:2517443/69‑1 (MQ=255)
                                cGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTTCACCAAGTTGTATATCTGCCTGACTATc                                     <  1:2573914/68‑1 (MQ=255)
                                cGTCCTCGCAGACTCCGTTCTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATc                                     <  1:2129788/68‑1 (MQ=255)
                                 gTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTAt                                      >  1:2780462/1‑66 (MQ=255)
                                 gTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATc                                     >  1:1610448/1‑67 (MQ=255)
                                 gTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATc                                     >  1:3010100/1‑67 (MQ=255)
                                 gTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATc                                     >  1:1198553/1‑67 (MQ=255)
                                      cGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTtcacca                                                            >  1:1028378/1‑39 (MQ=25)
                                      cGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTtcacca                                                            >  1:2685626/1‑39 (MQ=25)
                                      cGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTtcacca                                                            >  1:2871028/1‑39 (MQ=25)
                                      cGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTtcacca                                                            >  1:664687/1‑39 (MQ=25)
                                      cGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTtcacca                                                            >  1:518128/1‑39 (MQ=25)
                                      cGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTtcacca                                                            >  1:1651840/1‑39 (MQ=25)
                                      cGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTtcacca                                                            >  1:254144/1‑39 (MQ=25)
                                      cGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTtcacca                                                            >  1:2131180/1‑39 (MQ=25)
                                      cGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTtcacca                                                            >  1:2133491/1‑39 (MQ=25)
                                      cGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTtcacca                                                            >  1:1798222/1‑39 (MQ=25)
                                      cGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTtcacca                                                            >  1:2251672/1‑39 (MQ=25)
                                      cGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTtcacca                                                            >  1:229206/1‑39 (MQ=25)
                                      cGCAGACTCCGTTTTTGCCACTCGGCTTTGTCTtcacca                                                            >  1:159542/1‑39 (MQ=25)
                                         aGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGa                            <  1:3043318/68‑1 (MQ=255)
                                         aGACTACGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGa                            <  1:1297658/68‑1 (MQ=255)
                                              ccGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACa                                 >  1:3333259/1‑58 (MQ=255)
                                              ccGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGtgat                      >  1:1242561/1‑69 (MQ=255)
                                              ccGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGtgat                      >  1:3338304/1‑69 (MQ=255)
                                              ccGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGtgat                      >  1:2388000/1‑69 (MQ=255)
                                              ccGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGtgat                      <  1:2953168/69‑1 (MQ=255)
                                              ccGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGtgat                      <  1:2449066/69‑1 (MQ=255)
                                              ccGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGtgat                      >  1:2782360/1‑69 (MQ=255)
                                              ccGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGtgat                      >  1:1536323/1‑69 (MQ=255)
                                              ccGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACAATCTACAGCGGAGGtga                       >  1:1911333/1‑68 (MQ=255)
                                                          cTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAGTatg          <  1:471484/69‑1 (MQ=255)
                                                          cTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAGTatg          <  1:3167339/69‑1 (MQ=255)
                                                          cTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAGTatg          <  1:1545297/69‑1 (MQ=255)
                                                           tCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAg              <  1:929145/64‑1 (MQ=255)
                                                            cGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAg              <  1:627564/63‑1 (MQ=255)
                                                            cGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAg              <  1:655360/63‑1 (MQ=255)
                                                            cGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAg              <  1:1321805/63‑1 (MQ=255)
                                                            cGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAg              <  1:1651008/63‑1 (MQ=255)
                                                            cGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAg              <  1:816225/63‑1 (MQ=255)
                                                            cGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAg              <  1:2377972/63‑1 (MQ=255)
                                                            cGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAg              <  1:2523433/63‑1 (MQ=255)
                                                            cGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAg              <  1:2582267/63‑1 (MQ=255)
                                                            cGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAg              <  1:2631073/63‑1 (MQ=255)
                                                             ggCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAg              <  1:2062669/62‑1 (MQ=255)
                                                             ggCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAg              <  1:449696/62‑1 (MQ=255)
                                                                tttgctttCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAGTATGGATGGc    <  1:2432538/69‑1 (MQ=255)
                                                                    ctttCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAGTATGGATGGCGa  <  1:2672879/67‑1 (MQ=255)
                                                                    ctttCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAGTATGGATGGCGa  <  1:305396/67‑1 (MQ=255)
                                                                    ctttCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAGTATGGATGGCGa  <  1:1207428/67‑1 (MQ=255)
                                                                    ctttCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAGTATGGATGGCGa  <  1:1074673/67‑1 (MQ=255)
                                                                    |                                                                  
CATTCACTGCAATAAAGACGATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCACGTTGTATATCTGCCTGACTATCTACAGCGGAGGTGATGATGAAAGTATGGATGGCGA  >  minE/2520188‑2520322

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