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
A14 F1 I2 R1 774 49.2 2112398 96.9% 2046913 118.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,288,561 (C)7→6 pseudogene (354/2525 nt) yejO ← pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,288,5550C.100.0% 236.4 / NA 56pseudogene (360/2525 nt)yejOpseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (29/27);  total (29/27)

GACGGTTTGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGGCCCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATAACCG  >  NC_000913/2288420‑2288688
                                                                                                                                       |                                                                                                                                     
gaCGGTTTGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGGcccc                                                                                                                                    <  1:956293/139‑1 (MQ=255)
 aCGGTTTGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGGccccc                                                                                                                                   >  1:772547/1‑139 (MQ=255)
     tttGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGGccccccatc                                                                                                                               >  2:738688/1‑136 (MQ=255)
      ttGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGGccccccatct                                                                                                                              >  2:475576/1‑135 (MQ=255)
          tCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCttttt                                                                                                                         >  1:867869/1‑139 (MQ=255)
          tCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCGTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCttttt                                                                                                                         <  2:930745/139‑1 (MQ=255)
           ccGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTAATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGAAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCAACTTTTTc                                                                                                                        >  2:877110/1‑139 (MQ=255)
                          gCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTACCCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGcgccc                                                                                                         <  2:373986/139‑1 (MQ=255)
                          gCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGcgccc                                                                                                         <  2:867869/139‑1 (MQ=255)
                               cgTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCtt                                                                                                    <  1:239955/139‑1 (MQ=255)
                                                cACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTc                                                                                   >  1:311809/1‑139 (MQ=255)
                                                 aCCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCg                                                                                  >  2:540731/1‑139 (MQ=255)
                                                 aCCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCg                                                                                  >  2:1008423/1‑139 (MQ=255)
                                                    gCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAGCCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTg                                                                               <  2:493383/139‑1 (MQ=255)
                                                    gCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTg                                                                               <  2:2136/139‑1 (MQ=255)
                                                     ccTGCTTTCTGATCTACCGCAAATGTAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTgc                                                                              >  1:410840/1‑139 (MQ=255)
                                                     ccTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCt                                                                                                     >  2:37902/1‑116 (MQ=255)
                                                     ccTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCt                                                                                                     <  1:37902/116‑1 (MQ=255)
                                                     ccTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTgc                                                                              >  2:277025/1‑139 (MQ=255)
                                                         cTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCa                                                                          <  1:1014328/139‑1 (MQ=255)
                                                                aTCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCt                                                                   >  1:918914/1‑139 (MQ=255)
                                                                   tACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTa                                                                >  2:622998/1‑139 (MQ=255)
                                                                   tACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTa                                                                >  1:386929/1‑139 (MQ=255)
                                                                    aCCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAg                                                               <  2:311809/139‑1 (MQ=255)
                                                                    aCCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAg                                                               <  2:997262/139‑1 (MQ=255)
                                                                      cGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGca                                                             <  2:933851/139‑1 (MQ=255)
                                                                        caaatgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGcaca                                                           >  1:940648/1‑139 (MQ=255)
                                                                         aaatgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATaa                                                                       <  1:770030/126‑1 (MQ=255)
                                                                         aaatgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATaa                                                                       >  2:770030/1‑126 (MQ=255)
                                                                          aatgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACAcc                                                         >  1:1008467/1‑139 (MQ=255)
                                                                                 atCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTg                                                                                            >  1:346865/1‑97 (MQ=255)
                                                                                 atCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTg                                                                                            <  2:346865/97‑1 (MQ=255)
                                                                                     ccccTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCg                                              <  2:940648/139‑1 (MQ=255)
                                                                                              aaCCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGt                                     >  1:534572/1‑139 (MQ=255)
                                                                                                   ccAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGcc                                >  1:84217/1‑139 (MQ=255)
                                                                                                    cAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCa                                                                                                                       <  1:667398/51‑1 (MQ=255)
                                                                                                    cAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCa                                                                                                                       >  2:667398/1‑51 (MQ=255)
                                                                                                    cAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCcg                               >  2:251334/1‑139 (MQ=255)
                                                                                                    cAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCcg                               >  2:122620/1‑139 (MQ=255)
                                                                                                    cAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCcg                               >  2:242632/1‑139 (MQ=255)
                                                                                                    cAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTAAATCGTGGTATCATTCGCTGCGCCa                                                                          <  1:193077/96‑1 (MQ=255)
                                                                                                    cAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTAAATCGTGGTATCATTCGCTGCGCCa                                                                          >  2:193077/1‑96 (MQ=255)
                                                                                                       tagtCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCgcgc                            >  1:481330/1‑139 (MQ=255)
                                                                                                         gtCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCa                          <  2:166050/139‑1 (MQ=255)
                                                                                                         gtCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCa                          <  1:700670/139‑1 (MQ=255)
                                                                                                          tcctccCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGca                                                             <  2:877584/103‑1 (MQ=255)
                                                                                                          tcctccCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGca                                                             >  1:877584/1‑103 (MQ=255)
                                                                                                              cccTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCg                                                                                              >  1:700329/1‑66 (MQ=255)
                                                                                                              cccTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCg                                                                                              <  2:700329/66‑1 (MQ=255)
                                                                                                                    tCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAACGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAAc               <  1:475576/139‑1 (MQ=255)
                                                                                                                         aGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTg                                                                                            >  1:958539/1‑57 (MQ=255)
                                                                                                                         aGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTg                                                                                            <  2:958539/57‑1 (MQ=255)
                                                                                                                         aGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAAttt          >  2:274923/1‑139 (MQ=255)
                                                                                                                           cGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCg                                                                                              <  1:744864/53‑1 (MQ=255)
                                                                                                                           cGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCATTTAATCg                                                                                              >  2:744864/1‑53 (MQ=255)
                                                                                                                             aCAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATa      >  1:358642/1‑139 (MQ=255)
                                                                                                                             aCAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATa      >  2:95901/1‑139 (MQ=255)
                                                                                                                                 aGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATAACCg  <  1:1008423/139‑1 (MQ=255)
                                                                                                                                 aGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATAACCg  <  1:251334/139‑1 (MQ=255)
                                                                                                                                 aGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATAACCg  <  1:622998/139‑1 (MQ=255)
                                                                                                                                 aGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATAACCg  <  2:358642/139‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                     
GACGGTTTGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGGCCCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATAACCG  >  NC_000913/2288420‑2288688

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A