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 F1 I2 R1 766 55.6 2631458 94.7% 2491990 109.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,685,561 T→C intergenic (‑54/‑274) glyA ← / → hmp serine hydroxymethyltransferase/fused nitric oxide dioxygenase/dihydropteridine reductase 2

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,685,5610TC100.0% 251.4 / NA 68intergenic (‑54/‑274)glyA/hmpserine hydroxymethyltransferase/fused nitric oxide dioxygenase/dihydropteridine reductase 2
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (31/37);  total (31/37)

GACGTACTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCTGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCTTTGGAGAATAAAGAGCTTGCAACCGGAAACGGATTTCT  >  NC_000913/2685432‑2685696
                                                                                                                                 |                                                                                                                                       
gACGTACTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACaa                                                                                                                                >  1:1128867/1‑139 (MQ=255)
 aCGTACTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAAc                                                                                                                               >  1:653928/1‑139 (MQ=255)
     aCTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                           <  2:180650/139‑1 (MQ=255)
     aCTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                           <  2:653928/139‑1 (MQ=255)
     aCTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                           <  1:363219/139‑1 (MQ=255)
     aCTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                           >  1:341686/1‑139 (MQ=255)
     aCTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                           <  1:300445/139‑1 (MQ=255)
     aCTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                           >  1:180650/1‑139 (MQ=255)
     aCTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                           <  2:341686/139‑1 (MQ=255)
      cTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGa                                                                                                                          <  1:58126/139‑1 (MQ=255)
       tttttCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGaa                                                                                                                         <  1:1214582/139‑1 (MQ=255)
                     tAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGaa                                                                                                                         <  2:634487/125‑1 (MQ=255)
                     tAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGaa                                                                                                                         >  1:634487/1‑125 (MQ=255)
                     tAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGaa                                                                                                                         <  2:1079879/125‑1 (MQ=255)
                     tAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGaa                                                                                                                         >  1:1079879/1‑125 (MQ=255)
                          tGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATtg                                                                                                      >  1:21093/1‑139 (MQ=255)
                            ccACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATtgtg                                                                                                    >  2:800773/1‑139 (MQ=255)
                             cacaGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGc                                                                                                   <  2:313168/139‑1 (MQ=255)
                                       catcatAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGt                                                                                         <  2:1128867/139‑1 (MQ=255)
                                           atAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTg                                                                                     <  2:879798/139‑1 (MQ=255)
                                                    aaTGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACg                                                                                                                              >  1:897503/1‑89 (MQ=255)
                                                    aaTGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACg                                                                                                                              <  2:897503/89‑1 (MQ=255)
                                                    aaTGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGa                                                                                                                          <  2:16099/93‑1 (MQ=255)
                                                    aaTGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGa                                                                                                                          >  1:16099/1‑93 (MQ=255)
                                                         tCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTAc                                                                       >  1:443607/1‑139 (MQ=255)
                                                            tttCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCa                                                                    <  2:276269/139‑1 (MQ=255)
                                                            tttCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCa                                                                    <  1:836098/139‑1 (MQ=255)
                                                             ttCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCaa                                                                   >  2:941064/1‑139 (MQ=255)
                                                                 cGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                           <  1:407620/79‑1 (MQ=255)
                                                                 cGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                           >  2:407620/1‑79 (MQ=255)
                                                                 cGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGa                                                               <  1:1101951/139‑1 (MQ=255)
                                                                  gCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGAt                                                              <  2:21093/139‑1 (MQ=255)
                                                                    tttAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATaa                                                                                                                 >  1:681478/1‑86 (MQ=255)
                                                                    tttAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATaa                                                                                                                 <  2:681478/86‑1 (MQ=255)
                                                                    tttAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATaa                                                                                              <  1:1041964/105‑1 (MQ=255)
                                                                    tttAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATaa                                                                                              >  2:1041964/1‑105 (MQ=255)
                                                                      tAACATCCGCATCTCCTGACTCAGCTAACAATAAAGTTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACa                                                                                  <  2:797634/115‑1 (MQ=255)
                                                                      tAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACa                                                                                  >  1:797634/1‑115 (MQ=255)
                                                                       aaCATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACg                                                                                                                              <  1:172213/70‑1 (MQ=255)
                                                                       aaCATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACg                                                                                                                              >  2:172213/1‑70 (MQ=255)
                                                                        aCATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCtt                                                        <  1:941064/139‑1 (MQ=255)
                                                                            ccGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAAt                                                                                                           >  2:924530/1‑84 (MQ=255)
                                                                            ccGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAAt                                                                                                           <  1:924530/84‑1 (MQ=255)
                                                                            ccGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAAt                                                                                                           <  1:1088217/84‑1 (MQ=255)
                                                                            ccGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAAt                                                                                                           >  2:1088217/1‑84 (MQ=255)
                                                                            ccGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAgg                                                    >  2:323332/1‑139 (MQ=255)
                                                                             cGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGa                                                                                                                                   <  2:213912/59‑1 (MQ=255)
                                                                             cGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGa                                                                                                                                   >  1:213912/1‑59 (MQ=255)
                                                                                   tcCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCa                                             <  1:535759/139‑1 (MQ=255)
                                                                                    ccTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCaa                                            >  2:210171/1‑139 (MQ=255)
                                                                                      tGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAgg                                          <  1:907836/139‑1 (MQ=255)
                                                                                       gACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGc                                                                                                   <  2:397278/81‑1 (MQ=255)
                                                                                       gACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGc                                                                                                   >  1:397278/1‑81 (MQ=255)
                                                                                            aGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGaa                                                                                                                         >  2:305731/1‑54 (MQ=255)
                                                                                            aGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGaa                                                                                                                         <  1:305731/54‑1 (MQ=255)
                                                                                            aGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATaa                                                                                              >  1:66268/1‑81 (MQ=255)
                                                                                            aGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATaa                                                                                              <  2:66268/81‑1 (MQ=255)
                                                                                            aGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCTTTgg                                    <  1:800773/139‑1 (MQ=255)
                                                                                             gCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCttt                                      <  2:1135296/136‑1 (MQ=255)
                                                                                             gCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCttt                                      >  1:1135296/1‑136 (MQ=255)
                                                                                              cTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCTTTGgag                                  >  1:228574/1‑139 (MQ=255)
                                                                                                                             gTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGAt                                                              >  1:908001/1‑80 (MQ=255)
                                                                                                                             gTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGAt                                                              <  2:908001/80‑1 (MQ=255)
                                                                                                                             gTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCtt                                                        >  2:1100306/1‑86 (MQ=255)
                                                                                                                             gTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCtt                                                        <  1:1100306/86‑1 (MQ=255)
                                                                                                                             gTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCTTTGGAGAATAAAGAGCTTGCAACCGGAAACGGATTTc   >  2:960149/1‑139 (MQ=255)
                                                                                                                              tCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCTTTGGAGAATAAAGAGCTTGCAACCGGAAACGGATTTCt  <  1:1287292/139‑1 (MQ=255)
                                                                                                                              tCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCTTTGGAGAATAAAGAGCTTGCAACCGGAAACGGATTTCt  >  2:1153472/1‑139 (MQ=255)
                                                                                                                                 |                                                                                                                                       
GACGTACTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCTGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCTTTGGAGAATAAAGAGCTTGCAACCGGAAACGGATTTCT  >  NC_000913/2685432‑2685696

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A