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
A11 F28 I1 R1 228 65.7 2434974 91.7% 2232871 138.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,669,247 T→C R72R (CGT→CGC)  hcaE → putative 3‑phenylpropionate/cinnamate dioxygenase subunit alpha

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,669,2470TC96.3% 177.5 / ‑2.3 54R72R (CGT→CGC) hcaEputative 3‑phenylpropionate/cinnamate dioxygenase subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base C (26/26);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

ACCCGGATATTTACCAACTGGAGCTTGAGCGTATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGTCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTCTTATGGCATTAACGGCGAG  >  NC_000913/2669111‑2669382
                                                                                                                                        |                                                                                                                                       
aCCCGGATATTTACCAACTGGAGCTTGAGCGTATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAg                                                                                                                                      >  1:1035867/1‑140 (MQ=255)
aCCCGGATATTTACCAACTGGAGCTTGAGCGTATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAg                                                                                                                                      >  2:834218/1‑140 (MQ=255)
aCCCGGATATTTACCAACTGGAGCTTGAGCGTATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAg                                                                                                                                      >  1:912064/1‑140 (MQ=255)
   cGGATATTTACCAACTGGAGCTTGAGCGTATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGaaa                                                                                                                                   <  1:1040031/140‑1 (MQ=255)
            aCCAACTGGAGCTTGAGCGTATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGgcagc                                                                                                                          >  1:50879/1‑140 (MQ=255)
               aaCTGGAGCTTGAGCGTATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGTCAGAAAGACGGCAGCATc                                                                                                                       >  2:206907/1‑140 (MQ=255)
               aaCTGGAGCTTGAGCGTATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATc                                                                                                                       >  2:619246/1‑140 (MQ=255)
                aCTGGAGCTTGAGCGTATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCa                                                                                                                      >  2:97754/1‑140 (MQ=255)
                aCTGGAGCTTGAGCGTATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCa                                                                                                                      >  1:364415/1‑140 (MQ=255)
                    gAGCTTGAGCGTATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGc                                                                                                                  <  1:539817/140‑1 (MQ=255)
                       cTTGAGCGTATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGtt                                                                                                               >  1:1212796/1‑140 (MQ=255)
                               tATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAAcc                                                                                                       >  2:778297/1‑140 (MQ=255)
                                    tCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATgc                                                                                                  <  1:1004343/140‑1 (MQ=255)
                                            tGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCg                                                                                          >  2:76045/1‑140 (MQ=255)
                                              cTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCggg                                                                                        <  1:1121134/140‑1 (MQ=255)
                                                 gCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCACCACCGGGCCa                                                                                     <  2:142638/140‑1 (MQ=255)
                                                      ttCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCgt                                                                                <  1:663244/140‑1 (MQ=255)
                                                      ttCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCgt                                                                                <  2:360443/140‑1 (MQ=255)
                                                        ctcGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCgtgt                                                                              <  1:948741/140‑1 (MQ=255)
                                                           gCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAg                                                                           >  1:199658/1‑140 (MQ=255)
                                                           gCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAg                                                                           <  2:942470/140‑1 (MQ=255)
                                                                cGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATg                                                                      <  2:1035867/140‑1 (MQ=255)
                                                                  aaaGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCa                                                                    <  1:1133786/140‑1 (MQ=255)
                                                                    aGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGa                                                                  <  2:911208/140‑1 (MQ=255)
                                                                               aaaaCCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAaca                                                       >  1:911583/1‑140 (MQ=255)
                                                                                 aaCCCGTTGATTTCTTTAACCCCTACATGGGAGAAGATCGGGTTGTCTTGTTGCGCCAGAAAGACGGAAGCATCAAGGCGTTTCTCACCCAATGCCGCCACC‑GGCCATGCATGTGAGTTATGCAGATTGCGGCAACACTc                                                    <  2:531643/140‑1 (MQ=255)
                                                                                  aCCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTc                                                    <  1:1082279/140‑1 (MQ=255)
                                                                                      ggTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCgcgc                                                >  1:666866/1‑140 (MQ=255)
                                                                                      ggTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCgcgc                                                >  2:1173020/1‑140 (MQ=255)
                                                                                            ttCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTAc                                          <  2:199658/140‑1 (MQ=255)
                                                                                                 tAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGcc                                     <  2:666866/140‑1 (MQ=255)
                                                                                                    cacCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCGACACTCGCGCCTTTACCTGCCCGt                                  >  1:540007/1‑140 (MQ=255)
                                                                                                      ccTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTAt                                <  1:778297/140‑1 (MQ=255)
                                                                                                      ccTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTAt                                <  2:364415/140‑1 (MQ=255)
                                                                                                      ccTACATGGGAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTAt                                <  2:50879/140‑1 (MQ=255)
                                                                                                            tGGGAGAAGATGCGGTTGTCGTAGTGCGTCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGc                          <  1:206907/140‑1 (MQ=255)
                                                                                                             gggAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCt                         <  2:732282/140‑1 (MQ=255)
                                                                                                              ggAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACggttg                        <  2:685163/140‑4 (MQ=255)
                                                                                                              ggAGAAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTg                        >  2:922539/1‑140 (MQ=255)
                                                                                                               gagaAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGc                          >  2:296101/1‑137 (MQ=255)
                                                                                                               gagaAGATGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGc                          <  1:296101/137‑1 (MQ=255)
                                                                                                                 gaagaTGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTc                     >  2:674540/1‑140 (MQ=255)
                                                                                                                  aagaTGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGTCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTAt                                >  2:319243/1‑128 (MQ=255)
                                                                                                                  aagaTGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGTCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTAt                                <  1:319243/128‑1 (MQ=255)
                                                                                                                    gaTGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTCTTa                  >  2:915256/1‑140 (MQ=255)
                                                                                                                    gaTGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTCTTa                  >  1:450801/1‑140 (MQ=255)
                                                                                                                     aTGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTCTTAt                 >  1:913971/1‑140 (MQ=255)
                                                                                                                     aTGCGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTCTTAt                 >  1:359743/1‑140 (MQ=255)
                                                                                                                        cGGTTGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTCTTATGGc              >  2:676679/1‑140 (MQ=255)
                                                                                                                            tGTCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTCTTATGGCATTa          <  2:237559/140‑1 (MQ=255)
                                                                                                                              tCGTAGTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTCTTATGGCATTAAc        >  2:388404/1‑140 (MQ=255)
                                                                                                                                 tAGTGCGCCATAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTCTTATGGCATTAACGGc     <  1:834218/140‑1 (MQ=255)
                                                                                                                                   gTGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTCTTATGGCATTAACGGCGa   <  1:922539/140‑1 (MQ=255)
                                                                                                                                    tGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTCTTATGGCATTAACGGCGAg  <  2:911583/140‑1 (MQ=255)
                                                                                                                                    tGCGCCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTCTTATGGCATTAACGGCGAg  >  1:29989/1‑140 (MQ=255)
                                                                                                                                        |                                                                                                                                       
ACCCGGATATTTACCAACTGGAGCTTGAGCGTATTTTCGGTCGTTGCTGGCTATTTCTCGCCCACGAAAGCCAGATCCCAAAACCCGGTGATTTCTTTAACACCTACATGGGAGAAGATGCGGTTGTCGTAGTGCGTCAGAAAGACGGCAGCATCAAGGCGTTTCTCAACCAATGCCGCCACCGGGCCATGCGTGTGAGTTATGCAGATTGCGGCAACACTCGCGCCTTTACCTGCCCGTATCACGGCTGGTCTTATGGCATTAACGGCGAG  >  NC_000913/2669111‑2669382

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