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 1,977,299 G→A 53.2% intergenic (+53/‑42) sprT → / → endA conserved hypothetical protein/DNA‑specific endonuclease I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,977,2990GA53.2% 9.7 / 112.2 126intergenic (+53/‑42)sprT/endAconserved hypothetical protein/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base G (24/35);  new base A (48/19);  total (72/54)
Fisher's exact test for biased strand distribution p-value = 5.94e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

Only 100 of 126 total aligned reads displayed.

GCGAAATAACCATCTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTA  >  minE/1977238‑1977359
                                                             |                                                            
gCGAAATAACCATCTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGc                                                       <  1:1985660/69‑1 (MQ=255)
gCGAAATAACCATCTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGc                                                       <  1:1946696/69‑1 (MQ=255)
gCGAAATAACCATCTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGc                                                       <  1:3225949/69‑1 (MQ=255)
gCGAAATAACCATCTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGc                                                       <  1:3248709/69‑1 (MQ=255)
gCGAAATAACCATCTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGc                                                       <  1:1354716/69‑1 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCt                                          >  1:986574/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCt                                          >  1:438355/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGc                                           >  1:1492394/1‑68 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:60053/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:2036545/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:1990746/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:2998572/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:3003659/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:1240869/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:2180148/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:2436572/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:1516693/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:2197394/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:590348/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:1286994/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:494734/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:489143/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:1343140/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:2270408/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCt                                          >  1:2243965/1‑69 (MQ=255)
             cTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTAGCTGGCt                                          >  1:3042334/1‑69 (MQ=255)
              tGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGc                                                       <  1:1530277/55‑1 (MQ=255)
                   tATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGtttt                                    <  1:2356771/69‑1 (MQ=255)
                     tCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGtttt                                    <  1:2137528/67‑1 (MQ=255)
                     tCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTaa                                  >  1:866962/1‑69 (MQ=255)
                     tCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTaa                                  >  1:95075/1‑69 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:2285909/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:2658096/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:2863319/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:307910/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:2979144/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:2025148/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:1918319/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:1845809/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:1739576/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:1559095/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:415483/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:423386/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:487518/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:122540/69‑1 (MQ=255)
                             tttCCTGATCTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          <  1:1261368/69‑1 (MQ=255)
                                  tGATCTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      <  1:2417407/68‑1 (MQ=255)
                                  tGATCTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      <  1:3401609/68‑1 (MQ=255)
                                  tGATCTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      <  1:2097423/68‑1 (MQ=255)
                                   gATCTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTg                     <  1:1219463/68‑1 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGtt                                                 >  1:1498884/1‑37 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGt                          >  1:665633/1‑60 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      >  1:347012/1‑64 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      <  1:1380850/64‑1 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      <  1:1520366/64‑1 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      <  1:3264068/64‑1 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      <  1:1217519/64‑1 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      <  1:1476292/64‑1 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      >  1:2878365/1‑64 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      <  1:2674892/64‑1 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      >  1:3371359/1‑64 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      >  1:260486/1‑64 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      >  1:772482/1‑64 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      >  1:864890/1‑64 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      <  1:2427217/64‑1 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATg                  >  1:2490864/1‑68 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATg                  >  1:1520291/1‑68 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:625368/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:1412778/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:472919/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:1332347/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:504570/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:1079233/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:651680/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:758804/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:865768/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:972512/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:3321942/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:2185466/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:2445727/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:2141671/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:2957665/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:2096596/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:1934906/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:1865622/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:3193008/1‑69 (MQ=255)
                                      cTGGCTGATTGCATACCAAAACAACTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:3211064/1‑69 (MQ=255)
                                           tGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGt            <  1:881099/69‑1 (MQ=255)
                                           tGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGt            <  1:1129508/69‑1 (MQ=255)
                                           tGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGt            <  1:186542/69‑1 (MQ=255)
                                                   tACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTc    <  1:747738/69‑1 (MQ=255)
                                                     ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAacac                               >  1:1057340/1‑40 (MQ=255)
                                                     ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACg                              >  1:2369083/1‑41 (MQ=255)
                                                     ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACg                              >  1:2351905/1‑41 (MQ=255)
                                                     ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGt                 >  1:1964071/1‑54 (MQ=255)
                                                     ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTa  >  1:1140191/1‑69 (MQ=255)
                                                     ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTa  >  1:1297184/1‑69 (MQ=255)
                                                     ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTa  >  1:1711065/1‑69 (MQ=255)
                                                     ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTa  >  1:3307540/1‑69 (MQ=255)
                                                           cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGt                      <  1:3033837/43‑1 (MQ=255)
                                                             |                                                            
GCGAAATAACCATCTGAACTATCAGGAACTTTCCTGATCTGGCTGATTGCATACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTA  >  minE/1977238‑1977359

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