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
A6 F1 I2 R1 758 59.3 2864096 93.9% 2689386 105.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,457,718 A→G I448V (ATC→GTC)  gspD → general secretory pathway component, cryptic

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,457,7180AG98.5% 228.4 / NA 65I448V (ATC→GTC) gspDgeneral secretory pathway component, cryptic
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (33/31);  minor base T (1/0);  total (34/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

ACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATACCGTCGAACGCAAAACGGTGGGGACAAA  >  NC_000913/3457583‑3457845
                                                                                                                                       |                                                                                                                               
aCCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCg                                                                                                                              <  1:423405/139‑1 (MQ=255)
       cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGGTTACCGCGCTGACCAGTAACAATGAAAATGACATGCTCGCCACCCCAAGCGTCGTAACg                                                                                                                         >  2:912274/1‑137 (MQ=255)
       cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCt                                                                                                                       >  2:715460/1‑139 (MQ=255)
       cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCt                                                                                                                       >  1:762808/1‑139 (MQ=255)
       cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGACCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACg                                                                                                                         <  1:912274/137‑1 (MQ=255)
          aTCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACg                                                                                                                         >  2:1351678/1‑134 (MQ=255)
          aTCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACg                                                                                                                         <  1:1351678/134‑1 (MQ=255)
               gcctgGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGataata                                                                                                               >  2:915289/1‑139 (MQ=255)
                cctgGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATAACATCCTCGCCACCCCAAGCGTCGTAACGCTg                                                                                                                      <  1:1391163/131‑1 (MQ=255)
                cctgGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATAACATCCTCGCCACCCCAAGCGTCGTAACGCTg                                                                                                                      >  2:1391163/1‑131 (MQ=255)
                       tatGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTcgcg                                                                                                       <  1:915289/139‑1 (MQ=255)
                              aGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGCCTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCCCCCCAAGCGTCGTAACGCTGGATAAAAAACTCGCGTCCTTCa                                                                                                >  2:808921/1‑139 (MQ=255)
                               gcaccTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCaa                                                                                               >  1:428178/4‑139 (MQ=255)
                                  ccTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGt                                                                                            <  2:762808/139‑1 (MQ=255)
                                   cTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACg                                                                                                                         >  2:1335023/1‑109 (MQ=255)
                                   cTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACg                                                                                                                         <  1:1335023/109‑1 (MQ=255)
                                     aCAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTggg                                                                                         >  1:1207058/1‑139 (MQ=255)
                                     aCAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTggg                                                                                         >  1:837435/1‑139 (MQ=255)
                                        atggcatggcCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAATTCGCGTCCTTCAACGTGGGGCa                                                                                      <  1:715460/139‑1 (MQ=255)
                                               ggcCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTATCAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTcg                                                                                                         >  1:110330/1‑113 (MQ=255)
                                               ggcCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTcg                                                                                                         <  2:110330/113‑1 (MQ=255)
                                                gcCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGc                                                                              <  2:1207058/139‑1 (MQ=255)
                                                gcCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGc                                                                              <  2:53644/139‑1 (MQ=255)
                                                gcCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGc                                                                              <  2:837435/139‑1 (MQ=255)
                                                         ttcttcAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTAt                                                                     <  1:808921/139‑1 (MQ=255)
                                                           cttcAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATcc                                                                   >  1:781915/1‑139 (MQ=255)
                                                                 tGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCg                                                                            <  1:687060/124‑1 (MQ=255)
                                                                 tGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCg                                                                            >  2:687060/1‑124 (MQ=255)
                                                                     gACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAA‑GTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGAc                                                        <  2:428178/139‑1 (MQ=255)
                                                                      aCTGGGGAGTACTGCTTACCGCGCTGGCCAGTATCAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTg                                                                                                                      <  1:86698/77‑1 (MQ=255)
                                                                      aCTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTg                                                                                                                      >  2:86698/1‑77 (MQ=255)
                                                                          gggAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCg                                                                                                                              >  1:111048/1‑65 (MQ=255)
                                                                          gggAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCg                                                                                                                              <  2:111048/65‑1 (MQ=255)
                                                                                  tGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTg                                                                         <  1:262168/110‑1 (MQ=255)
                                                                                  tGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTg                                                                         >  2:262168/1‑110 (MQ=255)
                                                                                    cTTACCGGGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACg                                                                                                                         >  2:937233/1‑60 (MQ=255)
                                                                                    cTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACg                                                                                                                         <  1:937233/60‑1 (MQ=255)
                                                                                    cTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGa                                                                                                                    <  1:1292682/65‑1 (MQ=255)
                                                                                    cTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGa                                                                                                                    >  2:1292682/1‑65 (MQ=255)
                                                                                    cTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATa                                          >  1:51139/1‑139 (MQ=255)
                                                                                      tACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAAc                                        <  2:1073421/139‑1 (MQ=255)
                                                                                         cgcgCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGa                                                                                   <  2:1112211/93‑1 (MQ=255)
                                                                                         cgcgCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGa                                                                                   >  1:1112211/1‑93 (MQ=255)
                                                                                         cgcgCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTc                                     >  2:723272/1‑139 (MQ=255)
                                                                                           cgcTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCtt                                   >  2:570407/1‑139 (MQ=255)
                                                                                            gcTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGAc                                                        >  1:1148227/1‑117 (MQ=255)
                                                                                            gcTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGAc                                                        <  2:1148227/117‑1 (MQ=255)
                                                                                              tGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTc                                                  <  2:993631/121‑1 (MQ=255)
                                                                                              tGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTc                                                  >  1:993631/1‑121 (MQ=255)
                                                                                                          aTAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCgg                                                                           <  2:1013959/84‑1 (MQ=255)
                                                                                                          aTAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCgg                                                                           >  1:1013959/1‑84 (MQ=255)
                                                                                                          aTAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATCACGTCTTTAATACCGTCGAACg                    >  2:932109/1‑139 (MQ=255)
                                                                                                               aaTGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGAc                                                        <  2:416777/98‑1 (MQ=255)
                                                                                                               aaTGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGAc                                                        >  1:416777/1‑98 (MQ=255)
                                                                                                                  gACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATACCGTCg                        >  2:209129/1‑127 (MQ=255)
                                                                                                                  gACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATACCGTCg                        <  1:209129/127‑1 (MQ=255)
                                                                                                                   aCATCCTCGCCACCCCAAGCTTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATa                              >  2:840522/1‑120 (MQ=255)
                                                                                                                   aCATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCg                                                                  >  2:58568/1‑84 (MQ=255)
                                                                                                                   aCATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCg                                                                  <  1:58568/84‑1 (MQ=255)
                                                                                                                   aCATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTca                                                             >  2:501802/1‑89 (MQ=255)
                                                                                                                   aCATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTca                                                             <  1:501802/89‑1 (MQ=255)
                                                                                                                   aCATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATa                              <  1:840522/120‑1 (MQ=255)
                                                                                                                            ccACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGAGGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGCCTTTAATACCGTCTAACGCAAAACGGTAAGGACaaa  >  1:1017864/1‑139 (MQ=255)
                                                                                                                             cACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGAc                                                        >  2:348976/1‑84 (MQ=255)
                                                                                                                             cACCCCAAGCGTCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGAc                                                        <  1:348976/84‑1 (MQ=255)
                                                                                                                                       |                                                                                                                               
ACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCAACGTGGGGCAGGATGTGCCGGTGCTATCCGGGTCACAGACCACTTCAGGGGATAACGTCTTTAATACCGTCGAACGCAAAACGGTGGGGACAAA  >  NC_000913/3457583‑3457845

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A