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 2,582,467 A→G 51.0% Q196Q (CAA→CAG)  gadX → DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,582,4670AG51.0% 3.4 / 93.7 104Q196Q (CAA→CAG) gadXDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base A (21/30);  new base G (27/26);  total (48/56)
Fisher's exact test for biased strand distribution p-value = 3.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.37e-01

Only 100 of 110 total aligned reads displayed.

CTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCTGTGGA  >  minE/2582399‑2582530
                                                                    |                                                               
cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                                                                 >  1:314828/1‑69 (MQ=255)
cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                                                                 >  1:138586/1‑69 (MQ=255)
cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                                                                 >  1:82694/1‑69 (MQ=255)
cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                                                                 >  1:874854/1‑69 (MQ=255)
cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                                                                 >  1:1202394/1‑69 (MQ=255)
cTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCaa                                                                 >  1:886028/1‑69 (MQ=255)
     aaaGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGc                                                            >  1:3107855/1‑69 (MQ=255)
     aaaGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGc                                                            >  1:1997635/1‑69 (MQ=255)
     aaaGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGc                                                            >  1:1090697/1‑69 (MQ=255)
                tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                                 <  1:3163779/69‑1 (MQ=255)
                tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                                 <  1:1092441/69‑1 (MQ=255)
                tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                                 <  1:2769289/69‑1 (MQ=255)
                tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                                 <  1:2238066/69‑1 (MQ=255)
                tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                                 <  1:2880830/69‑1 (MQ=255)
                tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                                 <  1:961632/69‑1 (MQ=255)
                tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                                 <  1:2877622/69‑1 (MQ=255)
                tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                                 <  1:2425482/69‑1 (MQ=255)
                tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                                 <  1:736140/69‑1 (MQ=255)
                tGCGCGAAGAAGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                                 <  1:1009683/69‑1 (MQ=255)
                tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa                                                 <  1:1095540/69‑1 (MQ=255)
                tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa                                                 <  1:1394660/69‑1 (MQ=255)
                tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa                                                 <  1:1392105/69‑1 (MQ=255)
                tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa                                                 <  1:915022/69‑1 (MQ=255)
                tGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTa                                                 <  1:1100882/69‑1 (MQ=255)
                    cgAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCGACTTATTGt                                             <  1:601097/69‑1 (MQ=255)
                    cgAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGt                                             <  1:3372135/69‑1 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:2827488/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:2949311/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:551612/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:2607370/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:3181138/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:3185064/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:3186527/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:3250903/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:3304472/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:445362/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:2845648/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:797712/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:799209/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:833768/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:974132/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:2539672/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:1859140/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:2184999/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:1069935/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:1130849/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:1346411/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:165841/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:1393679/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:2188231/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:1538642/1‑54 (MQ=255)
                     gaagaaGGTACGTCATATTCACAGTTGCTTACAGAGTGTAGGATGCAGCGTGCt                                                           >  1:65563/1‑54 (MQ=255)
                       agaaggGATGTCATATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCt                                                           >  1:7542/1‑52 (MQ=255)
                            agaCATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATg                                     <  1:2048596/69‑1 (MQ=255)
                              aCATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGt                                             <  1:2415400/59‑1 (MQ=255)
                               cgtcatATTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTa                                                 <  1:1035248/52‑1 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                              <  1:1496901/69‑1 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                              <  1:573972/69‑1 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                              <  1:1357719/69‑1 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                              <  1:937589/69‑1 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                              <  1:3366496/69‑1 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                              <  1:2629520/69‑1 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                              <  1:2471229/69‑1 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                              <  1:2384279/69‑1 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                              <  1:2797691/69‑1 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                              <  1:2488976/69‑1 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGGATGCAGCGTGCTTTACAACTTATTGTTATATATGGGGTTTc                              <  1:2732758/69‑1 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTc                              >  1:3184646/1‑69 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTc                              >  1:2804168/1‑69 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTc                              >  1:1755911/1‑69 (MQ=255)
                                   atatTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTc                              >  1:1746125/1‑69 (MQ=255)
                                      ttCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCaa                            >  1:315050/1‑68 (MQ=255)
                                      ttCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCaa                            >  1:214687/1‑68 (MQ=255)
                                       tCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCa                             <  1:3257383/66‑1 (MQ=255)
                                       tCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCa                             <  1:3024973/66‑1 (MQ=255)
                                       tCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCa                             <  1:269722/66‑1 (MQ=255)
                                            gTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAgag                     <  1:2408986/69‑3 (MQ=255)
                                            gTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCg                     <  1:1966393/69‑1 (MQ=255)
                                                  tACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGc               <  1:805023/69‑1 (MQ=255)
                                                      gAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTa           <  1:1710618/69‑1 (MQ=255)
                                                      gAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTa           <  1:366480/69‑1 (MQ=255)
                                                      gAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTa           <  1:425087/69‑1 (MQ=255)
                                                           tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATcc        >  1:693137/1‑67 (MQ=255)
                                                           tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg      >  1:922724/1‑69 (MQ=255)
                                                           tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg      >  1:1332483/1‑69 (MQ=255)
                                                           tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg      >  1:817678/1‑69 (MQ=255)
                                                           tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg      >  1:1974799/1‑69 (MQ=255)
                                                           tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg      >  1:2850758/1‑69 (MQ=255)
                                                           tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg      >  1:787272/1‑69 (MQ=255)
                                                           tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg      >  1:574935/1‑69 (MQ=255)
                                                           tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg      >  1:3085785/1‑69 (MQ=255)
                                                           tAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtg      >  1:3123018/1‑69 (MQ=255)
                                                             gAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtgtg    <  1:771048/69‑1 (MQ=255)
                                                             gAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtgtg    <  1:2932429/69‑1 (MQ=255)
                                                             gAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtgtg    <  1:1708883/69‑1 (MQ=255)
                                                             gAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtgtg    <  1:34884/69‑1 (MQ=255)
                                                             gAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtgtg    <  1:3256873/69‑1 (MQ=255)
                                                             gAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtgtg    <  1:1048098/69‑1 (MQ=255)
                                                             gAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCtgtg    <  1:2688452/69‑1 (MQ=255)
                                                               aTGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCTGTGGa  <  1:1505549/69‑1 (MQ=255)
                                                                    |                                                               
CTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCTGTGGA  >  minE/2582399‑2582530

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