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
A12 F28 I1 R1 227 52.0 1764248 99.3% 1751898 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,666,093 T→C V220A (GTT→GCT)  csiE → stationary phase inducible protein CsiE

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,666,0930TC98.2% 190.7 / ‑4.2 56V220A (GTT→GCT) csiEstationary phase inducible protein CsiE
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (30/25);  total (31/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.18e-01

GCTGGGCGGAATCCTGCCTTGAATTTCAGGTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGTTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGATCAGCTT  >  NC_000913/2665964‑2666223
                                                                                                                                 |                                                                                                                                  
gCTGGGCGGAATCCTGCCTTGAATTTCAGGTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGGGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCa                                                                                                                          >  2:189640/1‑140 (MQ=255)
         aaTCCTGCCTTGAATTTCAGGTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGAt                                                                                                                 >  1:400810/1‑140 (MQ=255)
                ccTTGAATTTCAGGTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATc                                                                                                          >  2:169814/1‑140 (MQ=255)
                ccTTGAATTTCAGGTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATc                                                                                                          >  2:264019/1‑140 (MQ=255)
                   tGAATTTCAGGTAGCGCAGGAAATTGGACGCCACTGGCAGTGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGc                                                                                                       >  2:478493/1‑140 (MQ=255)
                    gAATTTCAGGTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCg                                                                                                      <  2:400810/140‑1 (MQ=255)
                          cAGGTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTCCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGgacag                                                                                                <  2:293123/140‑1 (MQ=255)
                                 cgcAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTg                                                                                         >  1:478547/1‑140 (MQ=255)
                                  gcAGGAAATTGGACGCCACTGGCAGTGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGc                                                                                        <  1:478493/140‑1 (MQ=255)
                                    aGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGt                                                                                      <  1:169814/140‑1 (MQ=255)
                                      aaaaTTGGCCGCCCCGGGCAGGGTCGGGCGCTCCAGCCTGT‑CCCCCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAg                                                                                   <  1:705117/139‑1 (MQ=255)
                                       aaaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAg                                                                                   <  1:182446/140‑1 (MQ=255)
                                        aaTTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGt                                                                                  <  2:446279/140‑1 (MQ=255)
                                                gCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCaaa                                                                          >  2:146392/1‑140 (MQ=255)
                                                  cACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACg                                                                        >  1:685253/1‑140 (MQ=255)
                                                   aCTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGt                                                                       <  2:478547/140‑1 (MQ=255)
                                                         aGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTa                                                                 >  2:475654/1‑140 (MQ=255)
                                                           cGTCGGGCGCTCCAGCCTGTACCACCTGATGGGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTaaa                                                               <  1:189640/140‑1 (MQ=255)
                                                            gTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAAc                                                              >  2:235967/1‑140 (MQ=255)
                                                            gTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAAc                                                              >  1:359947/1‑140 (MQ=255)
                                                            gTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAAc                                                              >  2:343654/1‑140 (MQ=255)
                                                                   gcTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTc                                                       <  2:359947/140‑1 (MQ=255)
                                                                       cAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGa                                                   >  2:30044/1‑140 (MQ=255)
                                                                          ccTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCt                                                <  1:30044/140‑1 (MQ=255)
                                                                                    cTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAATGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGtt                                      >  2:853963/1‑140 (MQ=255)
                                                                                        tgaGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGtt                                  >  2:478895/1‑140 (MQ=255)
                                                                                         gaGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGttt                                 <  1:146392/140‑1 (MQ=255)
                                                                                              aCTGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                            >  2:496627/1‑140 (MQ=255)
                                                                                                tGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                            <  2:381921/138‑1 (MQ=255)
                                                                                                tGTTTATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                            >  1:381921/1‑138 (MQ=255)
                                                                                                   ttATGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGaa                       <  1:235967/140‑1 (MQ=255)
                                                                                                     aTGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACa                     >  2:651298/1‑140 (MQ=255)
                                                                                                     aTGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACa                     >  2:196414/1‑140 (MQ=255)
                                                                                                      tGGCACTACTTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAg                    <  2:698186/140‑1 (MQ=255)
                                                                                                          actactTTTTTCCATGTTGCGGGTTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGt                >  1:134285/1‑140 (MQ=255)
                                                                                                          actactTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                            >  2:283889/1‑128 (MQ=255)
                                                                                                          actactTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                            >  1:178506/1‑128 (MQ=255)
                                                                                                          actactTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                            <  2:178506/128‑1 (MQ=255)
                                                                                                          actactTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTatg                            <  1:283889/128‑1 (MQ=255)
                                                                                                          actactTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGt                >  1:359165/1‑140 (MQ=255)
                                                                                                          actactTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGCTTTTatg                            >  2:514167/1‑128 (MQ=255)
                                                                                                          actactTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGCTTTTatg                            <  1:514167/128‑1 (MQ=255)
                                                                                                           ctactTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGtt               >  1:624682/1‑140 (MQ=255)
                                                                                                            tactTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGaa                       >  2:447137/1‑131 (MQ=255)
                                                                                                            tactTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGaa                       <  1:447137/131‑1 (MQ=255)
                                                                                                            tactTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTa              >  1:342055/1‑140 (MQ=255)
                                                                                                            tactTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTa              >  1:78342/1‑140 (MQ=255)
                                                                                                             actTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAt             <  1:445042/140‑1 (MQ=255)
                                                                                                              ctTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAggg                  >  2:759863/1‑134 (MQ=255)
                                                                                                              ctTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAggg                  <  1:759863/134‑1 (MQ=255)
                                                                                                              ctTTTTTCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTAtg            >  2:250330/1‑140 (MQ=255)
                                                                                                                  tttCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGAt        <  1:298735/140‑1 (MQ=255)
                                                                                                                  tttCCATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGAt        <  1:337057/140‑1 (MQ=255)
                                                                                                                      cATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGATCAGc    <  1:196414/140‑1 (MQ=255)
                                                                                                                      cATGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGATCAGc    <  1:343654/140‑1 (MQ=255)
                                                                                                                        tGTTGCGGGCTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGATCAGCtt  >  2:635500/1‑140 (MQ=255)
                                                                                                                                 |                                                                                                                                  
GCTGGGCGGAATCCTGCCTTGAATTTCAGGTAGCGCAGGAAATTGGACGCCACTGGCAGCGTCGGGCGCTCCAGCCTGTACCACCTGATGAGCCACTGTTTATGGCACTACTTTTTTCCATGTTGCGGGTTCCCGATCCATTGCGGGATGCGCATCAGCGGGACAGACAATTGCGTCAGTCTATCAAACGTCTGGTAAACCATTTTCGTGAGCTGGGAAATGTTCGTTTTTATGATGAACAGGGGTTATGTGATCAGCTT  >  NC_000913/2665964‑2666223

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A