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 2,582,431 A→G 44.4% T184T (ACA→ACG)  gadX → DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,582,4310AG44.4% 30.1 / 115.8 141T184T (ACA→ACG) gadXDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base A (26/52);  new base G (35/27);  total (62/79)
Fisher's exact test for biased strand distribution p-value = 9.79e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

Only 100 of 154 total aligned reads displayed.

CGAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATG  >  minE/2582366‑2582495
                                                                 |                                                                
cGAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               <  1:2424444/69‑1 (MQ=255)
cGAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               <  1:2700881/69‑1 (MQ=255)
 gAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatcat                                                              <  1:1389000/69‑1 (MQ=255)
 gAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatcat                                                              <  1:9394/69‑1 (MQ=255)
  aaTCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCata                                                             <  1:980247/69‑1 (MQ=255)
  aaTCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCata                                                             <  1:409189/69‑1 (MQ=255)
  aaTCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCata                                                             <  1:3150758/69‑1 (MQ=255)
  aaTCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCata                                                             <  1:1065568/69‑1 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               >  1:780311/1‑63 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               >  1:908036/1‑63 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               >  1:3227288/1‑63 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               >  1:467565/1‑63 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               >  1:1727380/1‑63 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           >  1:2934637/1‑67 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           >  1:3085261/1‑67 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:2766711/67‑1 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:28303/67‑1 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:2087421/67‑1 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           >  1:188726/1‑67 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:1814612/67‑1 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:3415282/67‑1 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:1163261/67‑1 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:1314138/67‑1 (MQ=255)
      gCCAGCGAGCTGTTGATGAGTCCAAGTCTCTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           <  1:1959453/67‑1 (MQ=255)
      gCCAGCGAGCTATTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATAtt                                                           >  1:765152/1‑67 (MQ=255)
      gCCACCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGAcatca                                                               >  1:300261/1‑63 (MQ=255)
        cAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTcac                                                        <  1:836434/68‑1 (MQ=255)
        cAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTcac                                                        <  1:3280360/68‑1 (MQ=255)
        cAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTcac                                                        <  1:1356107/68‑1 (MQ=255)
        cAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTcac                                                        <  1:3116921/68‑1 (MQ=255)
        cAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTcac                                                        <  1:3118240/68‑1 (MQ=255)
        cAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTcac                                                        <  1:2362766/68‑1 (MQ=255)
         aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:1651701/68‑1 (MQ=255)
         aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:904102/68‑1 (MQ=255)
         aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:818506/68‑1 (MQ=255)
         aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:30212/68‑1 (MQ=255)
         aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:2418869/68‑1 (MQ=255)
         aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:2343771/68‑1 (MQ=255)
         aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:215502/68‑1 (MQ=255)
         aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:1499171/68‑1 (MQ=255)
         aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:3320443/68‑1 (MQ=255)
         aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:1778072/68‑1 (MQ=255)
         aGCGAATTGTTGATGAGTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTcaca                                                       <  1:3324427/68‑1 (MQ=255)
                    gatgaGTCCAAGTCTGTTAAAGAAAAAATT‑‑GCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAg                                          <  1:353141/68‑1 (MQ=255)
                      tgaGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAg                                          <  1:3296103/68‑1 (MQ=255)
                      tgaGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAg                                          <  1:2924160/68‑1 (MQ=255)
                        aGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCata                                                             <  1:2944015/47‑1 (MQ=255)
                         gTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAgtgt                                       >  1:1048146/1‑68 (MQ=255)
                         gTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAgtgt                                       >  1:1809061/1‑68 (MQ=255)
                         gTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAgtgt                                       >  1:2640854/1‑68 (MQ=255)
                         gTCCAAGCCTGTTAAAGAAAAAATTGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAgtgt                                       >  1:263826/1‑68 (MQ=255)
                            cAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGaa                                   >  1:1065624/1‑69 (MQ=255)
                            cAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGaa                                   >  1:497549/1‑69 (MQ=255)
                              aGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAAt                                  >  1:2465143/1‑68 (MQ=255)
                              aGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAAt                                  >  1:639506/1‑68 (MQ=255)
                               gTCTGTTAAAGAAAAAATTGCGCGAAGAAGATACATCATATTCACAGTTGCTTACTGAGTGTAGAATGc                                <  1:3387706/69‑1 (MQ=255)
                               gTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGc                                <  1:2687939/69‑1 (MQ=255)
                                tCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCa                               <  1:1091868/69‑1 (MQ=255)
                                 cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTcac                                                        <  1:740008/43‑1 (MQ=255)
                                 cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                              >  1:886028/1‑69 (MQ=255)
                                 cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                              >  1:874854/1‑69 (MQ=255)
                                 cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                              >  1:138586/1‑69 (MQ=255)
                                 cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                              >  1:1202394/1‑69 (MQ=255)
                                      aaaGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAg                                          <  1:3099058/52‑1 (MQ=255)
                                      aaaGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGc                         >  1:1090697/1‑69 (MQ=255)
                                                 tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:736140/69‑1 (MQ=255)
                                                 tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:594515/69‑1 (MQ=255)
                                                 tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:1009683/69‑1 (MQ=255)
                                                 tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:812313/69‑1 (MQ=255)
                                                 tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:961632/69‑1 (MQ=255)
                                                 tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:2238066/69‑1 (MQ=255)
                                                 tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:2880830/69‑1 (MQ=255)
                                                 tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:2769289/69‑1 (MQ=255)
                                                 tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:3136936/69‑1 (MQ=255)
                                                 tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa              <  1:3163779/69‑1 (MQ=255)
                                                 tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa              <  1:1394660/69‑1 (MQ=255)
                                                 tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa              <  1:2138495/69‑1 (MQ=255)
                                                 tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa              <  1:1100882/69‑1 (MQ=255)
                                                 tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa              <  1:1095540/69‑1 (MQ=255)
                                                     cgAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGt          <  1:3372135/69‑1 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGAt                                  >  1:3064514/1‑44 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:2607370/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:2539672/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:833768/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:2827488/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:2949311/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:2845648/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:1859140/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:797712/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:1130849/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:2188231/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:3185064/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:551612/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:3186527/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:1393679/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:1538642/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:3250903/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                        >  1:165841/1‑54 (MQ=255)
                                                      gaagaaGGTACGTCATATTCACAGTTGCTTACAGAGTGTAGGATGCAGCGTGCt                        >  1:65563/1‑54 (MQ=255)
                                                             agaCATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATg  <  1:2048596/69‑1 (MQ=255)
                                                                 |                                                                
CGAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATG  >  minE/2582366‑2582495

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