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 1,926,217 G→A 62.8% V54I (GTA→ATA)  lysR → DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,926,2170GA62.8% 52.1 / 59.9 94V54I (GTA→ATA) lysRDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base G (11/24);  new base A (38/21);  total (49/45)
Fisher's exact test for biased strand distribution p-value = 2.72e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

Only 100 of 111 total aligned reads displayed.

CACAGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTGAAGAAGTGCAACGATCCTGG  >  minE/1926149‑1926282
                                                                    |                                                                 
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGATATTGTTTGAGcgcg                                                                   >  1:2038361/1‑69 (MQ=255)
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGcgcg                                                                   >  1:2333848/1‑69 (MQ=255)
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGcgcg                                                                   >  1:1767379/1‑69 (MQ=255)
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGcgcg                                                                   >  1:1554165/1‑69 (MQ=255)
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGcgcg                                                                   >  1:2986046/1‑69 (MQ=255)
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGcgcg                                                                   >  1:371961/1‑69 (MQ=255)
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGcgcg                                                                   >  1:1493079/1‑69 (MQ=255)
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGcgcg                                                                   >  1:1997245/1‑69 (MQ=255)
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGcgcg                                                                   >  1:2838557/1‑69 (MQ=255)
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGcgcg                                                                   >  1:1272155/1‑69 (MQ=255)
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGcgcg                                                                   >  1:2557620/1‑69 (MQ=255)
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGcgcg                                                                   >  1:907629/1‑69 (MQ=255)
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGcgcg                                                                   >  1:2200236/1‑69 (MQ=255)
cacaGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAAGTGATCGGGCTGAAATTGTTTGAGcgcg                                                                   >  1:1742549/1‑69 (MQ=255)
      catccGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTg                                                             <  1:2940770/66‑1 (MQ=255)
      cAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTg                                                             <  1:798886/69‑1 (MQ=255)
      cAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTg                                                             <  1:683972/69‑1 (MQ=255)
      cAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTg                                                             <  1:2939252/69‑1 (MQ=255)
      cAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTg                                                             <  1:1829460/69‑1 (MQ=255)
           gTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCg                                                         >  1:2054584/1‑68 (MQ=255)
           gTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCg                                                         >  1:1056198/1‑68 (MQ=255)
           gTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCg                                                         >  1:3310460/1‑68 (MQ=255)
           gTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCg                                                         >  1:1080474/1‑68 (MQ=255)
             cAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGAt                                                       >  1:1658232/1‑68 (MQ=255)
             cAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGAt                                                       >  1:391255/1‑68 (MQ=255)
             cAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGAt                                                       >  1:885075/1‑68 (MQ=255)
                ccGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTAc                                                    <  1:335243/68‑1 (MQ=255)
                ccGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACa                                                   <  1:77723/69‑1 (MQ=255)
                 cgcgAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACAt                                                  >  1:1216001/1‑69 (MQ=255)
                  gcgAACTTGCGCGCTTTGAGAAGGTGATCTGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACAt                                                  <  1:3080090/68‑1 (MQ=255)
                        tggcgctcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:2456249/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:702964/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:945830/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:2527831/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:2532581/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:280233/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:69235/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:513153/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:448398/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:3009250/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:1142609/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:1734373/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:1705307/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:2167019/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:1452194/56‑1 (MQ=255)
                        tggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTG‑TTGAGCGCATACGTGGACGAtt                                                      <  1:3076157/55‑1 (MQ=255)
                         ggcgcgcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:642743/56‑1 (MQ=255)
                              gcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAg                                     <  1:1508491/69‑1 (MQ=255)
                              gcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAg                                     <  1:1497441/69‑1 (MQ=255)
                              gcTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAg                                     <  1:1317028/69‑1 (MQ=255)
                               cTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAg                                     <  1:1512357/68‑1 (MQ=255)
                               cTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAg                                     <  1:1636784/68‑1 (MQ=255)
                               cTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAg                                     <  1:3022359/68‑1 (MQ=255)
                               cTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAg                                     <  1:2726996/68‑1 (MQ=255)
                                 ttGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGAtt                                                      <  1:325286/49‑1 (MQ=39)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAg                                     >  1:3264517/1‑65 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:3048806/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:3050184/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:3307109/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:3145605/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:3223679/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:187868/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:2775312/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:2066875/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:149535/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:617717/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:2608789/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:1293555/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:25324/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:849064/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:2524650/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:2498113/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:904886/1‑69 (MQ=255)
                                  tGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACt                                 >  1:2320828/1‑69 (MQ=255)
                                          tGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAGGACTGCGTCTg                          <  1:1062775/68‑1 (MQ=255)
                                          tGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAGGACTGCGTCTg                          <  1:2346847/68‑1 (MQ=255)
                                          tGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAGGACTGCGTCTg                          <  1:1782623/68‑1 (MQ=255)
                                          tGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAGGACTGCGTCTg                          <  1:2305661/68‑1 (MQ=255)
                                          tGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAGGACTGCGTCTg                          <  1:2746768/68‑1 (MQ=255)
                                               gggCTGGAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:437693/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGt                                          >  1:2466603/1‑47 (MQ=39)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:2706575/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:2417679/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:1121565/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:735632/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:1401018/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:1444412/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:2630477/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:3180815/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:2728534/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:2017561/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:1970789/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:155363/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:3317154/1‑68 (MQ=255)
                                               gggCTGAAATTGTTTGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTga                     >  1:3066329/1‑68 (MQ=255)
                                               gggCTGAAATTGTATGAGCGCATACGTGGACGATTACATCCTACCGTGCAAGGACTGCGTCTg                          >  1:626387/1‑63 (MQ=255)
                                                          gTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTGAAGAAGTGCAACg         >  1:210690/1‑69 (MQ=255)
                                                          gTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTGAAGAAGTGCAACg         >  1:2473669/1‑69 (MQ=255)
                                                                 cgcgTACGTGGGCGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTGAAGAAGTGCAACGATCCTgg  <  1:2789735/69‑1 (MQ=255)
                                                                 cgcgTACGTGGGCGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTGAAGAAGTGCAACGATCCTgg  <  1:2583304/69‑1 (MQ=255)
                                                                    |                                                                 
CACAGCCAACCGTCAGCCGCGAACTTGCGCGCTTTGAGAAGGTGATCGGGCTGAAATTGTTTGAGCGCGTACGTGGGCGATTACATCCTACCGTGCAAGGACTGCGTCTGTTTGAAGAAGTGCAACGATCCTGG  >  minE/1926149‑1926282

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