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 1,967,301 G→A 20.8% N443N (AAC→AAT)  tktA ← transketolase 1, thiamin‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,967,3010GA20.8% 213.3 / 39.6 143N443N (AAC→AAT) tktAtransketolase 1, thiamin‑binding
Reads supporting (aligned to +/- strand):  ref base G (64/49);  new base A (17/13);  total (81/62)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.66e-01

Only 100 of 143 total aligned reads displayed.

GAGTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGA  >  minE/1967242‑1967366
                                                           |                                                                 
gAGTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCATTACGTGCg                                                          <  1:3378603/69‑1 (MQ=255)
gAGTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCATTACGTGCg                                                          <  1:3122008/69‑1 (MQ=255)
gAGTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCATTACGTGCg                                                          <  1:2738253/69‑1 (MQ=255)
gAGTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCATTACGTGCg                                                          <  1:269923/69‑1 (MQ=255)
gAGTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCATTACGTGCg                                                          <  1:198128/69‑1 (MQ=255)
gAGTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCATTACGTGCg                                                          <  1:2479849/69‑1 (MQ=255)
gAGTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCATTACGTGCg                                                          <  1:1136711/69‑1 (MQ=255)
gAGTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCATTACGTGCg                                                          <  1:2444473/69‑1 (MQ=255)
gAGTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCATTACGTGCg                                                          <  1:2360904/69‑1 (MQ=255)
gAGTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCATTACGTGCg                                                          <  1:768507/69‑1 (MQ=255)
  ggcGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGt                                                         <  1:2156557/66‑1 (MQ=255)
  gTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGt                                                         <  1:3363798/68‑1 (MQ=255)
  gTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGt                                                         <  1:2626089/68‑1 (MQ=255)
           gtAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGaa                                               <  1:1168365/69‑1 (MQ=255)
               aCCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGt                                                         <  1:2041417/55‑1 (MQ=255)
               aCCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATc                                           >  1:1490218/1‑69 (MQ=255)
               aCCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATc                                           >  1:277926/1‑69 (MQ=255)
               aCCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATc                                           >  1:1538275/1‑69 (MQ=255)
                ccATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCa                                          <  1:2071970/69‑1 (MQ=255)
                ccATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCa                                          <  1:1794324/69‑1 (MQ=255)
                     aCCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAg                                     >  1:1486836/1‑69 (MQ=255)
                     aCCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAg                                     >  1:2282488/1‑69 (MQ=255)
                     aCCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAg                                     >  1:2311964/1‑69 (MQ=255)
                     aCCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAg                                     >  1:500915/1‑69 (MQ=255)
                     aCCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAg                                     >  1:370053/1‑69 (MQ=255)
                     aCCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAg                                     >  1:1256459/1‑69 (MQ=255)
                     aCCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAg                                     >  1:2737966/1‑69 (MQ=255)
                     aCCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAg                                     >  1:3293296/1‑69 (MQ=255)
                     aCCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAg                                     >  1:2845609/1‑69 (MQ=255)
                         gACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTgg                                 >  1:1345938/1‑69 (MQ=255)
                         gACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTgg                                 >  1:1375132/1‑69 (MQ=255)
                         gACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTgg                                 >  1:456307/1‑69 (MQ=255)
                         gACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTgg                                 >  1:3048372/1‑69 (MQ=255)
                         gACGCTGTTTCATCAGCGCAGCCATACGTACGGAGTTACGTGCGTATTCCACGAACATCAGGAAGGTgg                                 >  1:3375279/1‑69 (MQ=255)
                            gCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGa                                <  1:2712218/67‑1 (MQ=255)
                            gCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGa                                <  1:3319299/67‑1 (MQ=255)
                            gCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGa                                <  1:36107/67‑1 (MQ=255)
                            gCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGa                                <  1:238439/67‑1 (MQ=255)
                            gCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGa                                <  1:2896500/67‑1 (MQ=255)
                            gCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGa                                <  1:921454/67‑1 (MQ=255)
                            gCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGa                                <  1:644712/67‑1 (MQ=255)
                            gCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGa                                <  1:2144938/67‑1 (MQ=255)
                            gCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGa                                <  1:1952468/67‑1 (MQ=255)
                            gCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGa                                <  1:1050743/67‑1 (MQ=255)
                              tGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGgtg                            <  1:1680033/69‑1 (MQ=255)
                                    atcaGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACgg                       <  1:1280915/68‑1 (MQ=255)
                                    atcaGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACgg                       <  1:1666147/68‑1 (MQ=255)
                                    atcaGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACgg                       <  1:638361/68‑1 (MQ=255)
                                    atcaGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACgg                       <  1:516776/68‑1 (MQ=255)
                                    atcaGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACgg                       <  1:441632/68‑1 (MQ=255)
                                     tcaGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGc                      <  1:898456/68‑1 (MQ=255)
                                          gcAGCCATACGTACGGCGTTACGTGCGTATTCCACGaa                                               <  1:2305669/38‑1 (MQ=255)
                                           cAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCa                                          <  1:565531/42‑1 (MQ=255)
                                           cAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACgg                       <  1:2060797/61‑1 (MQ=255)
                                              ccATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCAc            <  1:3237480/69‑1 (MQ=255)
                                              ccATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCAc            <  1:225568/69‑1 (MQ=255)
                                              ccATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCAc            <  1:1532550/69‑1 (MQ=255)
                                                aTACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGa                                <  1:12187/47‑1 (MQ=255)
                                                aTACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCg          <  1:467976/69‑1 (MQ=255)
                                                aTACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCg          <  1:1186083/69‑1 (MQ=255)
                                                  acgtacgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACgg                       <  1:2047933/54‑1 (MQ=255)
                                                   cgtacgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGc       >  1:2834233/1‑69 (MQ=255)
                                                   cgtacgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGc       >  1:1232464/1‑69 (MQ=255)
                                                   cgtacgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGc       >  1:481113/1‑69 (MQ=255)
                                                   cgtacgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGc       >  1:774761/1‑69 (MQ=255)
                                                   cgtacgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGc       >  1:739081/1‑69 (MQ=255)
                                                   cgtacgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGc       >  1:2013352/1‑69 (MQ=255)
                                                   cgtacgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGc       >  1:1463850/1‑69 (MQ=255)
                                                   cgtacgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGc       >  1:2632517/1‑69 (MQ=255)
                                                   cgtacgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGc       >  1:1044099/1‑69 (MQ=255)
                                                   cgtacgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGc       >  1:1517445/1‑69 (MQ=255)
                                                   cgtacgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGc       >  1:1879283/1‑69 (MQ=255)
                                                   cgtacgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGc       >  1:3430074/1‑69 (MQ=255)
                                                       cgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGc       >  1:72575/1‑65 (MQ=255)
                                                       cgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCa      >  1:3287133/1‑66 (MQ=255)
                                                       cgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCa      >  1:395066/1‑66 (MQ=255)
                                                       cgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCa      >  1:559052/1‑66 (MQ=255)
                                                       cgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCa      >  1:684896/1‑66 (MQ=255)
                                                       cgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCa      >  1:864522/1‑66 (MQ=255)
                                                       cgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCa      >  1:1009842/1‑66 (MQ=255)
                                                       cgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCa      >  1:3351895/1‑66 (MQ=255)
                                                       cgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCa      >  1:1321400/1‑66 (MQ=255)
                                                       cgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCa      >  1:1432079/1‑66 (MQ=255)
                                                       cgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCa      >  1:2391771/1‑66 (MQ=255)
                                                       cgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCa      >  1:194863/1‑66 (MQ=255)
                                                       cgGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCa      >  1:2955332/1‑66 (MQ=255)
                                                        ggCATTACGTGCGTATTCCACGAACATCAGGAAGGTTGAGGTATACGGCAGGAACCCACCGTGCa      >  1:2062800/1‑65 (MQ=25)
                                                        ggCATTACGTGCGTATTCCACGAACATCAGGAAGGTTGAGGTATACGGCAGGAAACCa             >  1:1128751/1‑58 (MQ=21)
                                                        ggCATTACGTGCGTATTCCACGAACATCAGGAAGGTTGAGGTATACGGCAGGAAACCACCGTGc       >  1:2418803/1‑64 (MQ=21)
                                                        ggCATTACGTGCGTATTCCACGAACATCAGGAAGGTTGAGGTATACGGCAGGAAACCACCGTGCa      >  1:2231823/1‑65 (MQ=25)
                                                        ggCATTACGTGCGTATTCCACGAACATCAGGAAGGTTGAGGTATACGGCAGGAAACCACCGTGCa      >  1:825122/1‑65 (MQ=25)
                                                        ggCATTACGTGCGTATTCCACGAACATCAGGAAGGTTGAGGTATACGGCAGGAAACCACCGTGCa      >  1:1754035/1‑65 (MQ=25)
                                                        ggCATTACGTGCGTATTCCACGAACATCAGGAAGGTTGAGGTATACGGCAGGAAACCACCGTGCa      >  1:3024757/1‑65 (MQ=25)
                                                        ggCATTACGTGCGTATTCCACGAACATCAGGAAGGTTGAGGTATACGGCAGGAAACCACCGTGCa      >  1:3038353/1‑65 (MQ=25)
                                                        ggCATTACGTGCGTATTCCACGAACATCAGGAAGGTTGAGGTATACGGCAGGAAACCACCGTGCa      >  1:3117644/1‑65 (MQ=25)
                                                        ggCATTACGTGCGTATTCCACGAACATCAGGAAGGTTGAGGTATACGGCAGGAAACCACCGTGCa      >  1:3199734/1‑65 (MQ=25)
                                                        ggCATTACGTGCGTATTCCACGAACATCAGGAAGGTTGAGGTATACGGCAGGAAACCACCGTGCa      >  1:106018/1‑65 (MQ=25)
                                                        ggCATTACGTGCGTATTCCACGAACATCAGGAAGGTTGAGGTATACGGCAGGAAACCACCGTGCa      >  1:1160558/1‑65 (MQ=25)
                                                        ggCATTACGTGCGTATTCCACGAACATCAGGAAGGTTGAGGTATACGGCAGGAAACCACCGTGCAggg   >  1:2326529/1‑68 (MQ=25)
                                                          cGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGga  <  1:1012078/67‑1 (MQ=255)
                                                           |                                                                 
GAGTCGTGGGTGTAAACCATCACCTGACGCTGTTTCATCAGCGCAGCCATACGTACGGCGTTACGTGCGTATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGA  >  minE/1967242‑1967366

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