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 2,582,461 A→G 44.6% R194R (AGA→AGG)  gadX → DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,582,4610AG44.6% 23.4 / 100.1 121R194R (AGA→AGG) gadXDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base A (32/35);  new base G (28/26);  total (60/61)
Fisher's exact test for biased strand distribution p-value = 7.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01

Only 100 of 124 total aligned reads displayed.

CAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCTGTG  >  minE/2582394‑2582528
                                                                   |                                                                   
cAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGaa                                                                    >  1:497549/1‑69 (MQ=255)
cAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGaa                                                                    >  1:1065624/1‑69 (MQ=255)
cAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGaa                                                                    >  1:1369002/1‑69 (MQ=255)
  aGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAAt                                                                   >  1:1869737/1‑68 (MQ=255)
  aGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAAt                                                                   >  1:639506/1‑68 (MQ=255)
  aGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAAt                                                                   >  1:786002/1‑68 (MQ=255)
  aGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAAt                                                                   >  1:670743/1‑68 (MQ=255)
   gTCTGTTAAAGAAAAAATTGCGCGAAGAAGATACATCATATTCACAGTTGCTTACTGAGTGTAGAATGc                                                                 <  1:3387706/69‑1 (MQ=255)
   gTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGc                                                                 <  1:1631240/69‑1 (MQ=255)
   gTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGc                                                                 <  1:2687939/69‑1 (MQ=255)
   gTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGc                                                                 <  1:3435216/69‑1 (MQ=255)
   gTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGc                                                                 <  1:1061208/69‑1 (MQ=255)
    tCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCa                                                                <  1:1091868/69‑1 (MQ=255)
     cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                                                               >  1:1202394/1‑69 (MQ=255)
     cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                                                               >  1:874854/1‑69 (MQ=255)
     cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                                                               >  1:886028/1‑69 (MQ=255)
     cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                                                               >  1:82694/1‑69 (MQ=255)
     cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                                                               >  1:138586/1‑69 (MQ=255)
     cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                                                               >  1:314828/1‑69 (MQ=255)
          aaaGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGc                                                          >  1:1997635/1‑69 (MQ=255)
          aaaGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGc                                                          >  1:3107855/1‑69 (MQ=255)
          aaaGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGc                                                          >  1:1090697/1‑69 (MQ=255)
                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                               <  1:2425482/69‑1 (MQ=255)
                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                               <  1:3163779/69‑1 (MQ=255)
                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                               <  1:3136936/69‑1 (MQ=255)
                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                               <  1:2769289/69‑1 (MQ=255)
                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                               <  1:2880830/69‑1 (MQ=255)
                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                               <  1:2877622/69‑1 (MQ=255)
                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                               <  1:1009683/69‑1 (MQ=255)
                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                               <  1:736140/69‑1 (MQ=255)
                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                               <  1:961632/69‑1 (MQ=255)
                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                               <  1:1092441/69‑1 (MQ=255)
                     tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                               <  1:812313/69‑1 (MQ=255)
                     tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa                                               <  1:2138495/69‑1 (MQ=255)
                     tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa                                               <  1:1095540/69‑1 (MQ=255)
                     tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa                                               <  1:1394660/69‑1 (MQ=255)
                     tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa                                               <  1:1392105/69‑1 (MQ=255)
                         cgAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCGACTTATTGt                                           <  1:601097/69‑1 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGAt                                                                   >  1:3064514/1‑44 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:2845648/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:551612/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:974132/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:833768/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:3185064/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:3186527/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:799209/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:3250903/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:3304472/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:797712/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:445362/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:2827488/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:1130849/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:1538642/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:165841/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:1859140/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:2184999/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:2188231/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:2539672/1‑54 (MQ=255)
                          gaagaaGGTACGTCATATTCACAGTTGCTTACAGAGTGTAGGATGCAGCGTGCt                                                         >  1:65563/1‑54 (MQ=255)
                            agaaggGATGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                         >  1:7542/1‑52 (MQ=255)
                                   aCATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGt                                           <  1:2415400/59‑1 (MQ=255)
                                    cgtcatATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                               <  1:1035248/52‑1 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                            <  1:2488976/69‑1 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                            <  1:2471229/69‑1 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                            <  1:2797691/69‑1 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                            <  1:1496901/69‑1 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                            <  1:1357719/69‑1 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                            <  1:3366496/69‑1 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                            <  1:2384279/69‑1 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                            <  1:2629520/69‑1 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                            <  1:1313481/69‑1 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                            <  1:937589/69‑1 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                            <  1:573972/69‑1 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTc                            >  1:3184646/1‑69 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTc                            >  1:1746125/1‑69 (MQ=255)
                                        atatTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTc                            >  1:2804168/1‑69 (MQ=255)
                                           ttCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCaa                          >  1:214687/1‑68 (MQ=255)
                                           ttCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCaa                          >  1:315050/1‑68 (MQ=255)
                                            tCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCa                           <  1:269722/66‑1 (MQ=255)
                                            tCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCa                           <  1:3024973/66‑1 (MQ=255)
                                            tCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCa                           <  1:3257383/66‑1 (MQ=255)
                                                 gTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAgag                   <  1:2408986/69‑3 (MQ=255)
                                                 gTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCg                   <  1:1966393/69‑1 (MQ=255)
                                                       tACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGc             <  1:3274567/69‑1 (MQ=255)
                                                       tACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGc             <  1:805023/69‑1 (MQ=255)
                                                           gAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTa         <  1:366480/69‑1 (MQ=255)
                                                           gAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTa         <  1:1710618/69‑1 (MQ=255)
                                                                tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg    >  1:922724/1‑69 (MQ=255)
                                                                tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg    >  1:2850758/1‑69 (MQ=255)
                                                                tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg    >  1:2506119/1‑69 (MQ=255)
                                                                tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg    >  1:1332483/1‑69 (MQ=255)
                                                                tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg    >  1:3085785/1‑69 (MQ=255)
                                                                tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg    >  1:574935/1‑69 (MQ=255)
                                                                tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg    >  1:1974799/1‑69 (MQ=255)
                                                                  gAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtgtg  <  1:2932429/69‑1 (MQ=255)
                                                                  gAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtgtg  <  1:1708883/69‑1 (MQ=255)
                                                                  gAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtgtg  <  1:771048/69‑1 (MQ=255)
                                                                  gAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtgtg  <  1:2688452/69‑1 (MQ=255)
                                                                  gAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtgtg  <  1:1048098/69‑1 (MQ=255)
                                                                  gAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtgtg  <  1:34884/69‑1 (MQ=255)
                                                                   |                                                                   
CAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCTGTG  >  minE/2582394‑2582528

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