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
A9 F1 I1 R1 759 71.0 3673240 91.5% 3361014 104.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,439,141 C→T *123* (TAG→TAA)  yhdN ← DUF1992 family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,439,1410CT100.0% 203.9 / NA 65*123* (TAG→TAA) yhdNDUF1992 family protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (34/31);  total (34/31)

ATAGGCGAAACCCACCTTCAGTACGCACTTCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCACTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCTAACCTCTTGATATTGCGGATCATC  >  NC_000913/3439013‑3439275
                                                                                                                                |                                                                                                                                      
ataGGCGAAACCCACCTTCAGTACGCACTTCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGt                                                                                                                              <  1:1174373/139‑1 (MQ=255)
    gCGAAACCCACCTTCAGTACGCACTTCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGAt                                                                                                                          >  2:1551626/1‑139 (MQ=255)
     cGAAACCCACCTTCAGTACGCACTTCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGAtt                                                                                                                         >  1:1330795/1‑139 (MQ=255)
      gAAACCCACCTTCAGTACGCACTTCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGAttt                                                                                                                        <  1:1611249/139‑1 (MQ=255)
       aaaCCCACCTTCAGTACGCACTTCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGAtttt                                                                                                                       >  1:513055/1‑139 (MQ=255)
         aCCCACCTTCAGTACGCACTTCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGt                                                                                                                     >  2:1258479/1‑139 (MQ=255)
                   aGTACGCACTTCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACtt                                                                                                           <  1:264790/139‑1 (MQ=255)
                      aCGCACTTCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTc                                                                                                        <  2:1330795/139‑1 (MQ=255)
                       cGCACTTCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACt                                                                                                            >  1:1724723/1‑134 (MQ=255)
                       cGCACTTCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACt                                                                                                            <  2:1724723/134‑1 (MQ=255)
                         cACTTCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGc                                                                                                     >  2:254430/1‑139 (MQ=255)
                             tCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATaa                                                                                                 >  1:1605682/1‑139 (MQ=255)
                               aTGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGAttt                                                                                                                        <  1:70410/114‑1 (MQ=255)
                               aTGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGAttt                                                                                                                        >  2:70410/1‑114 (MQ=255)
                               aTGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATc                                                                                               >  1:1459748/1‑139 (MQ=255)
                                    ccATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTc                                                                                                        <  2:602484/125‑1 (MQ=255)
                                    ccATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTc                                                                                                        >  1:602484/1‑125 (MQ=255)
                                      atcatcTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGt                                                                                        >  1:1633765/1‑139 (MQ=255)
                                         atcTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTaaa                                                                                     <  1:254430/139‑1 (MQ=255)
                                             gctgTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAAt                                                                                 >  1:42307/1‑139 (MQ=255)
                                               tgTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGtt                                                                                                                                   >  2:959908/1‑87 (MQ=255)
                                               tgTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGtt                                                                                                                                   <  1:959908/87‑1 (MQ=255)
                                                 tttttCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTcc                                                                                                                   <  1:1356209/101‑1 (MQ=255)
                                                 tttttCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTcc                                                                                                                   >  2:1356209/1‑101 (MQ=255)
                                                    ttCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACt                                                                          <  1:1258479/139‑1 (MQ=255)
                                                             aCGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGc                                                                 <  2:1459748/139‑1 (MQ=255)
                                                                     tgtCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGc                                                                 <  1:212956/131‑1 (MQ=255)
                                                                     tgtCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGc                                                                 >  2:212956/1‑131 (MQ=255)
                                                                            tgtTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTcc                                                                                                                   <  2:441742/74‑1 (MQ=255)
                                                                            tgtTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTcc                                                                                                                   >  1:441742/1‑74 (MQ=255)
                                                                             gtTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAAt                                                 <  1:1551626/139‑1 (MQ=255)
                                                                               tACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTc                                               >  2:1612633/1‑139 (MQ=255)
                                                                                aCTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGAtt                                                                                                                         <  2:1087415/64‑1 (MQ=255)
                                                                                aCTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGAtt                                                                                                                         >  1:1087415/1‑64 (MQ=255)
                                                                                aCTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTcc                                              >  1:723277/1‑139 (MQ=255)
                                                                                aCTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATAGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTcc                                              >  2:530682/1‑139 (MQ=255)
                                                                                    ccGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTa                                          >  2:758943/1‑139 (MQ=255)
                                                                                      gCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGAtt                                                                                                                         >  2:1564098/1‑58 (MQ=255)
                                                                                      gCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGAtt                                                                                                                         <  1:1564098/58‑1 (MQ=255)
                                                                                      gCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAAtt                                                >  1:891612/1‑131 (MQ=255)
                                                                                      gCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAAtt                                                <  2:891612/131‑1 (MQ=255)
                                                                                      gCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAAt                                        >  2:964639/1‑139 (MQ=255)
                                                                                                    cTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCt                          <  2:1605682/139‑1 (MQ=255)
                                                                                                    cTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCt                          <  2:1633765/139‑1 (MQ=255)
                                                                                                    cTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCt                          >  2:196833/1‑139 (MQ=255)
                                                                                                    cTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCt                          <  1:964639/139‑1 (MQ=255)
                                                                                                    cTCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCt                          <  1:196833/139‑1 (MQ=255)
                                                                                                     tCACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCTa                         <  2:513055/139‑1 (MQ=255)
                                                                                                      cACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCg                                                                               <  2:907538/84‑1 (MQ=255)
                                                                                                      cACCAATGCGATACATACATACTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCg                                                                               >  1:907538/1‑84 (MQ=255)
                                                                                                                 tacatacatacTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTc                                                                                                        <  2:1783184/48‑1 (MQ=255)
                                                                                                                 tacatacatacTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTc                                                                                                        >  1:1783184/1‑48 (MQ=255)
                                                                                                                 tacatacatacTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCTAACCTCTTGatat             >  2:1031354/1‑139 (MQ=255)
                                                                                                                        atacTCCGTTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAGTCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCt                          >  1:1198838/1‑119 (MQ=255)
                                                                                                                        atacTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCt                          <  2:1198838/119‑1 (MQ=255)
                                                                                                                        atacTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCTAACCTCTTGATATTGCGGat      <  2:42307/139‑1 (MQ=255)
                                                                                                                         tacTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCt                          <  1:709016/118‑1 (MQ=255)
                                                                                                                         tacTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCt                          >  2:709016/1‑118 (MQ=255)
                                                                                                                           cTCCATTAGTTATTGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTa                                                                            <  2:1238665/66‑1 (MQ=255)
                                                                                                                           cTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTa                                                                            >  1:1238665/1‑66 (MQ=255)
                                                                                                                           cTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAAtt                                                >  2:107422/1‑94 (MQ=255)
                                                                                                                           cTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAAtt                                                <  1:107422/94‑1 (MQ=255)
                                                                                                                           cTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCTAACCTCTTGATATTGCGGatcat   >  1:977860/1‑139 (MQ=255)
                                                                                                                           cTCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCTAACCTCTTGATATTGCGGatcat   >  2:865133/1‑139 (MQ=255)
                                                                                                                            tCCATTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCTAACCTCTTGATATTGCGGatcatc  <  1:1612633/139‑1 (MQ=255)
                                                                                                                                |                                                                                                                                      
ATAGGCGAAACCCACCTTCAGTACGCACTTCATGCTCCATCATCTGCTGTTTTTCGTAATAACGAATCGTGTCGGGTGTTACTTCCGCCATTTTTGCCAGCTCACCAATGCGATACATACATACTCCACTAGTTATCGTTGATTTTGTCCAACAACTTGTCAGCATAATCGCCGCGTAAAAAATCGGTACTCAATCCAGCTTGTCGCAGCTTCAATTCCAGTAATGACAATCGACGGCTAACCTCTTGATATTGCGGATCATC  >  NC_000913/3439013‑3439275

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A