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
A3 F108 I0 R1 42 64.6 1127642 98.1% 1106216 264.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 876,148 C→T 13.8% R272C (CGC→TGC)  yliF → putative membrane‑anchored diguanylate cyclase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913876,1480CT13.8% 71.5 / 4.0 29R272C (CGC→TGC) yliFputative membrane‑anchored diguanylate cyclase
Reads supporting (aligned to +/- strand):  ref base C (14/11);  new base T (2/2);  total (16/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGATGTTCTCTCTATTTAAGAACGGTAAACCGGTGACCGGTGATGAATATAATGCTAAAAACGCCATCTTCACCGTTTCGGAAGCGATGGAGCACTTCGCCTATTTGCCGACCGGATTGTATGTATTTGCGTATAAAAAAGATGTTTATTTGCGGGTTTGTACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATGAAAGTGGTGAAAATCCTTAAATCACAGATCCCGGTAGATAAAGGTAAAG  >  NC_000913/875860‑876427
                                                                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                                                       
cTGATTTTCTCTCTATTTAAGACCGGTAATCCGGTGACCGGTGATGAATATAATGCTAAAAACGCCATCTTCACCGTTTCGGAAGCGATGGAGAACTTCGCCTATTTGCCGACCGGATTGTATGTATTTGCGTATAAAAAAGATGTTTATTTGCGGGTTTGTACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAAc                                                                                                                                                                                                                                                                                         <  2:8372/289‑1 (MQ=255)
         tctctATTTAAGAACGGTAAACCGGTGACCGGTGATGAATATAATGCTAAAAACGCCATCTTCACCGTTTCGGAAGCGATGGAGCACTTCGCCTATTTGCCGACCGGATTGTATGTATTTGCGTATAAAAAAGATGTTTATTTGCGGGTTTGTACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAATGCGTACTgg                                                                                                                                                                                                                                                                                >  1:10619/1‑289 (MQ=255)
                                    accggtgaTGAATATAATGCTAAAAACGCCATCTTCACCGTTTCGGAAGCGATGGAGCACTTCGCCTATTTGCCGACCGGATTGTATGTATTTGCGTATAAAAAAGATGTTTATTTGCGGGTTTGTACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCg                                                                                                                                                                                                                                                     >  2:557551/1‑289 (MQ=255)
                                     ccggtgaTGAATATAATGCTAAAAACGCCATCTTCACCGTTTCGGAAGCGATGGAGCACTTCGCCTATTTGCCGACCGGATTGTATGTATTTGCGTATAAAAAAGATGTTTATTTGCGGGTTTGTACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGa                                                                                                                                                                                                                                                    <  1:222252/289‑1 (MQ=255)
                                                      gCTAAAATCGCCATCTTAACTGTTTCGGTAGCGATGTAGCATTTCGCCTATTTGCCGACCGGATTGTATGTATTTGCGTATCAAGAAGATGTTTATTTGCGGGTTTGTTCATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACa                                                                                                                                                                                                                                   <  1:540973/289‑1 (MQ=255)
                                                      gCTAAAAACGCCATCTTCACCGTTTCGGAAGCGATGGAGCACTTCGCCTATTTGCCGACCGGATTGTATGTATTTGCGTATAAAAAAGATGTTTATTTGCGGGTTTGTACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAATGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACa                                                                                                                                                                                                                                   <  2:10619/289‑1 (MQ=255)
                                                                     ttCACCGTTTCGGAAGCGATGGAGCACTTCGCCTATTTGCCGACCGGATTGTATGTATTTGCGTATAAAAAAGATGTTTATTTGCGGGTTTGTACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCgg                                                                                                                                                                                                                    <  1:557551/289‑1 (MQ=255)
                                                                                   aGCGATGGAGCACTTCGCCTATTTGCCGACCGGATTGTATGTATTTGCGTATAAAAAAGATGTTTATTTGCGGGTTTGTACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGgacgac                                                                                                                                                                                                      <  2:18522/289‑1 (MQ=255)
                                                                                      gATGGAGCACTTCGCCTATTTGCCGACCGGATTGTATGTATTTGCGTATAAAAAAGATGTTTATTTGCGGGTTTGTACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCt                                                                                                                                                                                                    <  1:112556/288‑1 (MQ=255)
                                                                                                                                      taAAAAAGATGTTTATTTGCGGGTTTGTACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCt                                                                                                                                                    >  1:286912/1‑288 (MQ=255)
                                                                                                                                                       tGCGGGTTTGTACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGCAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTa                                                                                                                                  >  1:454759/1‑289 (MQ=255)
                                                                                                                                                                 tACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTgg                                                                                                                                                                                                           >  2:61345/1‑206 (MQ=255)
                                                                                                                                                                 tACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTgg                                                                                                                                                                                                           <  1:61345/206‑1 (MQ=255)
                                                                                                                                                                      tGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTg                                                                                                                    >  2:537479/1‑288 (MQ=255)
                                                                                                                                                                                   tGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGa                                                                                                                                                                                                                                                    >  1:178532/1‑147 (MQ=255)
                                                                                                                                                                                   tGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGa                                                                                                                                                                                                                                                    <  2:178532/147‑1 (MQ=255)
                                                                                                                                                                                                              tGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCAt                                                                           >  1:431978/1‑289 (MQ=255)
                                                                                                                                                                                                                   gTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCAttt                                                                         >  1:251185/1‑286 (MQ=255)
                                                                                                                                                                                                                               tGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAgt                                                          <  1:537479/289‑1 (MQ=255)
                                                                                                                                                                                                                                  tACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCCTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGtt                                                       >  1:32170/1‑289 (MQ=255)
                                                                                                                                                                                                                                     gCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCt                                                                      >  1:199138/1‑271 (MQ=255)
                                                                                                                                                                                                                                     gCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCt                                                                      <  2:199138/271‑1 (MQ=255)
                                                                                                                                                                                                                                         agTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAATGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGaa                                                            <  1:152151/277‑1 (MQ=255)
                                                                                                                                                                                                                                         agTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAATGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGaa                                                            >  2:152151/1‑277 (MQ=255)
                                                                                                                                                                                                                                         agTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAACGCAAAGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTTCCGGAAAAAGGCGGTTACTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTCCGTTCATTTGCTGGGCTATGAAGTGTTGATCaaa                                                >  2:543668/1‑289 (MQ=255)
                                                                                                                                                                                                                                         agTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATGaaa                                                >  2:507502/1‑289 (MQ=255)
                                                                                                                                                                                                                                                     tGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATa                                                                                                           >  2:53098/1‑218 (MQ=255)
                                                                                                                                                                                                                                                     tGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATa                                                                                                           <  1:53098/218‑1 (MQ=255)
                                                                                                                                                                                                                                                                            tcatTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATGAAAGTGGTGAAAATCCTTAAATCACAGATCCCGGTAGa             <  1:542742/289‑1 (MQ=255)
                                                                                                                                                                                                                                                                                         ttttGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATGAAAGTGGTGAAAATCCTTAAATCACAGATCCCGGTAGATAAAGGTAAAg  >  1:209808/1‑287 (MQ=255)
                                                                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                                                       
CTGATGTTCTCTCTATTTAAGAACGGTAAACCGGTGACCGGTGATGAATATAATGCTAAAAACGCCATCTTCACCGTTTCGGAAGCGATGGAGCACTTCGCCTATTTGCCGACCGGATTGTATGTATTTGCGTATAAAAAAGATGTTTATTTGCGGGTTTGTACATTGATTATTTTCTTTGCCGCATTGGTGGCAGTGATATCGGGTGCCAGTTGCCTCTATCTGGTACGCAGAGTGATTAATCGTGGTATTGTGGAGAAAGAAGCCATCATTAATAACCATTTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATGAAAGTGGTGAAAATCCTTAAATCACAGATCCCGGTAGATAAAGGTAAAG  >  NC_000913/875860‑876427

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A