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 2,582,428 G→T 39.6% E183D (GAG→GAT) ‡ gadX → DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,582,4280GT39.6% 121.3 / 134.6 159E183D (GAG→GAT) ‡gadXDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base G (37/59);  new base T (35/28);  total (72/87)
Fisher's exact test for biased strand distribution p-value = 5.03e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01

Only 100 of 161 total aligned reads displayed.

AGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATG  >  minE/2582362‑2582495
                                                                  |                                                                   
aGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAgaga                                                                    >  1:2441034/1‑68 (MQ=255)
aGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAc                                                                   >  1:2041802/1‑69 (MQ=255)
aGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAc                                                                   >  1:178768/1‑69 (MQ=255)
aGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAc                                                                   >  1:3072214/1‑69 (MQ=255)
    cGAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               <  1:2700881/69‑1 (MQ=255)
     gAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatcat                                                              <  1:9394/69‑1 (MQ=255)
     gAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               <  1:902800/68‑1 (MQ=255)
      aaTCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCata                                                             <  1:3150758/69‑1 (MQ=255)
      aaTCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCata                                                             <  1:1449535/69‑1 (MQ=255)
      aaTCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCata                                                             <  1:1806884/69‑1 (MQ=255)
      aaTCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCata                                                             <  1:409189/69‑1 (MQ=255)
      aaTCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCata                                                             <  1:1065568/69‑1 (MQ=255)
      aaTCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCata                                                             <  1:980247/69‑1 (MQ=255)
        tCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           >  1:1853104/1‑69 (MQ=255)
        tCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           >  1:2089172/1‑69 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               >  1:3219800/1‑63 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               >  1:1727380/1‑63 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               >  1:467565/1‑63 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               >  1:780311/1‑63 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               >  1:908036/1‑63 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:28303/67‑1 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           >  1:188726/1‑67 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:2087421/67‑1 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           >  1:2934637/1‑67 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:2611066/67‑1 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:2659464/67‑1 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:2766711/67‑1 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           >  1:1694617/1‑67 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:839444/67‑1 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:1314138/67‑1 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:3415282/67‑1 (MQ=255)
          gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           >  1:3085261/1‑67 (MQ=255)
          gCCACCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               >  1:300261/1‑63 (MQ=255)
            cAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTcac                                                        <  1:3116921/68‑1 (MQ=255)
            cAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTcac                                                        <  1:836434/68‑1 (MQ=255)
            cAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTcac                                                        <  1:2362766/68‑1 (MQ=255)
            cAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTcac                                                        <  1:2469610/68‑1 (MQ=255)
             aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:2418869/68‑1 (MQ=255)
             aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:1174257/68‑1 (MQ=255)
             aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:3324427/68‑1 (MQ=255)
             aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:2343771/68‑1 (MQ=255)
             aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:215502/68‑1 (MQ=255)
                          tgaGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAg                                          <  1:2924160/68‑1 (MQ=255)
                          tgaGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAg                                          <  1:3296103/68‑1 (MQ=255)
                            aGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCata                                                             <  1:2944015/47‑1 (MQ=255)
                             gTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACTTCATATTCACAGTTGCTTACTGAgtgt                                       >  1:3119699/1‑68 (MQ=255)
                             gTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAgtgt                                       >  1:3018889/1‑68 (MQ=255)
                             gTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAgtgt                                       >  1:1048146/1‑68 (MQ=255)
                             gTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAgtgt                                       >  1:2640854/1‑68 (MQ=255)
                             gTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAgtgt                                       >  1:1809061/1‑68 (MQ=255)
                             gTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAgtgt                                       >  1:112057/1‑68 (MQ=255)
                                cAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGaa                                   >  1:1065624/1‑69 (MQ=255)
                                cAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGaa                                   >  1:1369002/1‑69 (MQ=255)
                                cAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGaa                                   >  1:497549/1‑69 (MQ=255)
                                  aGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAgtg                                        >  1:3276379/1‑62 (MQ=255)
                                  aGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAAt                                  >  1:670743/1‑68 (MQ=255)
                                  aGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAAt                                  >  1:639506/1‑68 (MQ=255)
                                  aGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAAt                                  >  1:786002/1‑68 (MQ=255)
                                   gTCTGTTAAAGAAAAAATTGCGCGAAGAAGATACATCATATTCACAGTTGCTTACTGAGTGTAGAATGc                                <  1:3387706/69‑1 (MQ=255)
                                   gTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGc                                <  1:1631240/69‑1 (MQ=255)
                                   gTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGc                                <  1:3435216/69‑1 (MQ=255)
                                     cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                              >  1:82694/1‑69 (MQ=255)
                                     cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                              >  1:886028/1‑69 (MQ=255)
                                     cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                              >  1:138586/1‑69 (MQ=255)
                                     cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                              >  1:314828/1‑69 (MQ=255)
                                          aaaGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGc                         >  1:3107855/1‑69 (MQ=255)
                                          aaaGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGc                         >  1:1997635/1‑69 (MQ=255)
                                          aaaGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGc                         >  1:1090697/1‑69 (MQ=255)
                                                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:736140/69‑1 (MQ=255)
                                                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:2769289/69‑1 (MQ=255)
                                                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:812313/69‑1 (MQ=255)
                                                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:1092441/69‑1 (MQ=255)
                                                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:961632/69‑1 (MQ=255)
                                                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:1009683/69‑1 (MQ=255)
                                                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:2880830/69‑1 (MQ=255)
                                                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:2425482/69‑1 (MQ=255)
                                                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:2238066/69‑1 (MQ=255)
                                                     tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa              <  1:1392105/69‑1 (MQ=255)
                                                     tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa              <  1:1394660/69‑1 (MQ=255)
                                                     tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa              <  1:1095540/69‑1 (MQ=255)
                                                         cgAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCGACTTATTGt          <  1:601097/69‑1 (MQ=255)
                                                         cgAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGt          <  1:3372135/69‑1 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGAt                                  >  1:3064514/1‑44 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:2827488/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:2845648/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:2607370/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:2949311/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:2188231/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:799209/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:1859140/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:1130849/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:165841/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:3181138/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:3185064/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:551612/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:1538642/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:1346411/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:3250903/1‑54 (MQ=255)
                                                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:3304472/1‑54 (MQ=255)
                                                            agaaggGATGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:7542/1‑52 (MQ=255)
                                                                  |                                                                   
AGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATG  >  minE/2582362‑2582495

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