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
A13 F1 I1 R1 778 68.7 3228504 93.4% 3015422 109.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,775,526 G→A S368N (AGC→AAC)  mtlD → mannitol‑1‑phosphate dehydrogenase, NAD‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,775,5260GA98.4% 195.4 / ‑4.6 62S368N (AGC→AAC) mtlDmannitol‑1‑phosphate dehydrogenase, NAD‑dependent
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (25/36);  total (25/37)
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

ACCTGATTGAAGGTATTGCCGCTGCAATGCACTTCCGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAGCGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGATTGTCAGATATGCAGGCAACAATGGAACAAACCCAGGCCTTTGAAAA  >  NC_000913/3775391‑3775660
                                                                                                                                       |                                                                                                                                      
aCCTGATTGAAGGTATTGCCGCTGCAATGCACTTCCGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGa                                                                                                                                     >  2:1328906/1‑139 (MQ=255)
aCCTGATTGAAGGTATTGCCGCTGCAATGCACTTCCGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTCATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGa                                                                                                                                     >  1:1151411/1‑139 (MQ=255)
   ggcttGAAGGGATTGCCGCTGCGATGTGCTTCTTGTGGGTAGAGGATCCGCAGGCTCAGGAACTGGTGGGGGCGATCGCGGACAAAGGTCCTCAGGCGGCGCTGGCCCAGATTTCCGGTGTTGATGCCAACTGCGTGGt                                                                                                                                  <  1:216393/136‑1 (MQ=255)
                     cTGCAATGCACTTCCGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAAc                                                                                                                <  2:1529081/139‑1 (MQ=255)
                      tGCAATGCACTTCCGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAAcc                                                                                                               <  2:395148/139‑1 (MQ=255)
                      tGCAATGCACTTCCGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAAcc                                                                                                               <  2:52392/139‑1 (MQ=255)
                           tGCACTTCCGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTta                                                                                                          <  1:351114/139‑1 (MQ=255)
                                ttCCGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAAcc                                                                                                               <  2:1468424/129‑1 (MQ=255)
                                ttCCGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAAcc                                                                                                               >  1:1468424/1‑129 (MQ=255)
                                ttCCGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAg                                                                                                     <  2:644759/139‑1 (MQ=255)
                                ttCCGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAg                                                                                                     <  1:917906/139‑1 (MQ=255)
                                ttCCGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAg                                                                                                     <  1:1271368/139‑1 (MQ=255)
                                  ccGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAAcc                                                                                                               >  1:1535236/1‑127 (MQ=255)
                                  ccGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAAcc                                                                                                               <  2:1535236/127‑1 (MQ=255)
                                   cGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAgcaa                                                                                                  <  2:769270/139‑1 (MQ=255)
                                   cGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAgcaa                                                                                                  <  1:1161607/139‑1 (MQ=255)
                                     cAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAg                                                                                                     >  1:990584/1‑134 (MQ=255)
                                     cAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAg                                                                                                     >  1:1287864/1‑134 (MQ=255)
                                     cAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAg                                                                                                     <  2:1287864/134‑1 (MQ=255)
                                     cAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAg                                                                                                     <  2:990584/134‑1 (MQ=255)
                                       gTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAgcaatgca                                                                                              >  2:417254/1‑139 (MQ=255)
                                            gatgatCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATcc                                                                                                                           <  2:427939/105‑1 (MQ=255)
                                            gatgatCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATcc                                                                                                                           >  1:427939/1‑105 (MQ=255)
                                            gatgatCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCaataat                                                                                         >  2:1209646/1‑139 (MQ=255)
                                                  ccGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAgg                                                                                                                                   >  2:1474117/1‑91 (MQ=255)
                                                  ccGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAgg                                                                                                                                   <  1:1474117/91‑1 (MQ=255)
                                                  ccGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTtata                                                                                                        >  2:1377423/1‑118 (MQ=255)
                                                  ccGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTtata                                                                                                        <  1:1377423/118‑1 (MQ=255)
                                                    gCAGGCTCAGGAACTGGCAGCACTGAACGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGAcc                                                                                 <  2:449261/139‑1 (MQ=255)
                                                      aGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAg                                                                                                     <  1:94053/117‑1 (MQ=255)
                                                      aGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAg                                                                                                     >  2:94053/1‑117 (MQ=255)
                                                      aGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGActgt                                                                               <  2:1151411/139‑4 (MQ=255)
                                                       ggCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAgg                                                                              >  1:1050438/1‑139 (MQ=255)
                                                        gCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGgc                                                                             <  1:1100865/139‑1 (MQ=255)
                                                             ggAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAgg                                                                        >  2:790303/1‑139 (MQ=255)
                                                              gAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGa                                                                       <  1:1328906/139‑1 (MQ=255)
                                                                       gcaCTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTgcg                                                              >  2:698717/1‑139 (MQ=255)
                                                                        caCTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTgcgc                                                             <  1:790303/139‑1 (MQ=255)
                                                                          cTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGccc                                                           <  2:579775/139‑1 (MQ=255)
                                                                            gATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATcc                                                                                                                           >  2:837520/1‑73 (MQ=255)
                                                                            gATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATcc                                                                                                                           <  1:837520/73‑1 (MQ=255)
                                                                              tCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAAt                                                       <  1:279180/139‑1 (MQ=255)
                                                                                     cAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGAt                                                >  1:1286283/1‑139 (MQ=255)
                                                                                      aaaGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGAtt                                               <  2:832364/139‑1 (MQ=255)
                                                                                       aaGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATaa                                                     <  1:45050/132‑1 (MQ=255)
                                                                                       aaGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATaa                                                     >  2:45050/1‑132 (MQ=255)
                                                                                       aaGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGATTg                                              >  2:218978/1‑139 (MQ=255)
                                                                                               cAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGATTGTCAGatat                                      >  1:218938/1‑139 (MQ=255)
                                                                                                aGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGATTGTCAGATATg                                     <  2:1286283/139‑1 (MQ=255)
                                                                                                    ggcgCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAAtggt                                                                                      <  1:1248502/86‑1 (MQ=255)
                                                                                                    ggcgCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAAtggt                                                                                      >  2:1248502/1‑86 (MQ=255)
                                                                                                    ggcgCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGa                                                 >  2:479241/1‑123 (MQ=255)
                                                                                                    ggcgCTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGa                                                 <  1:479241/123‑1 (MQ=255)
                                                                                                     gcgcTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGATTGTCAGATATGCAGGc                                <  2:384569/139‑1 (MQ=255)
                                                                                                     gcgcTGGCACAGATTTCCGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGATTGTCAGATATGCAGGc                                <  1:698717/139‑1 (MQ=255)
                                                                                                                gATTTCCGGTCCTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGATTGTCAGATATGCAGGCAACAATGGAAc                     <  2:1050438/139‑1 (MQ=255)
                                                                                                                     ccGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAAGCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGATTGTCAGATATGCAGGCAACAATGGAACAAAcc                >  2:1053331/1‑139 (MQ=255)
                                                                                                                     ccGGTCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGATTGTCAGATATGCAGGCAACAATGGAACAAAcc                <  1:417254/139‑1 (MQ=255)
                                                                                                                         tCTTGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGATTGTCAGATATGCAGGCAACAATGGAACAAACCCAgg            <  2:218938/139‑1 (MQ=255)
                                                                                                                           ttGATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGATTGTCAGATATGCAGGCAACAATGGAACAAACCCAGGcc          >  1:923278/1‑139 (MQ=255)
                                                                                                                             gATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAg                                                                               >  1:208665/1‑68 (MQ=255)
                                                                                                                             gATGCCAACAACGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAg                                                                               <  2:208665/68‑1 (MQ=255)
                                                                                                                                   aacaacGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGATTGTCAGATATGCAGGCAACAATGGAACAAACCCAGGCCTTTGaaaa  <  2:923278/139‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                      
ACCTGATTGAAGGTATTGCCGCTGCAATGCACTTCCGCAGTGAAGATGATCCGCAGGCTCAGGAACTGGCAGCACTGATCGCTGACAAAGGTCCGCAGGCGGCGCTGGCACAGATTTCCGGTCTTGATGCCAACAGCGAGGTTGTATCCGAGGCGGTAACCGCTTATAAAGCAATGCAATAATGGTGGACCAGGCGCAGGACACCCTGCGCCCGAATAACAGATTGTCAGATATGCAGGCAACAATGGAACAAACCCAGGCCTTTGAAAA  >  NC_000913/3775391‑3775660

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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