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
A4 F28 I1 R1 100 74.7 2540932 99.2% 2520604 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,015,515 (T)7→8 intergenic (+56/‑200) pqiC → / → rmf intermembrane transport lipoprotein PqiC/ribosome modulation factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,015,5081.T97.7% 128.5 / ‑3.4 43intergenic (+49/‑207)pqiC/rmfintermembrane transport lipoprotein PqiC/ribosome modulation factor
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base T (16/26);  total (17/26)
Fisher's exact test for biased strand distribution p-value = 3.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGATGGTTACGATGAGATGGTTAAAGTGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GG‑TTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACAAATATGACAGTGGCGTGAATTTTGCGCATTGACGGCAGTTATGATTCGCGGTA  >  NC_000913/1015369‑1015639
                                                                                                                                             |                                                                                                                                   
ggATGGTTACGATGAGATGGTTAAAGTGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑gg                                                                                                                                      >  1:424320/1‑140 (MQ=255)
ggATGGTTACGATGAGATGGTTAAAGTGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑gg                                                                                                                                      >  1:340006/1‑140 (MQ=255)
     gTTACGATGAGATGGTTAAAGTGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GG‑ttttt                                                                                                                                >  2:901088/1‑140 (MQ=255)
       tACGATGAGATGGTTAAAGTGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GG‑ttttttt                                                                                                                              <  2:340006/140‑1 (MQ=255)
       tACGATGAGATGGTTAAAGTGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GG‑ttttttt                                                                                                                              >  2:672462/1‑140 (MQ=255)
       tACGATGAGATGGTTAAAGTGCTGGCCGATGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GG‑ttttttt                                                                                                                              <  2:555337/140‑1 (MQ=255)
               gaTGGTTAAAGTGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTa                                                                                                                       >  1:184630/1‑140 (MQ=255)
               gaTGGTTAAAGTGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTa                                                                                                                       <  1:1092745/140‑1 (MQ=255)
                aTGGTTAAAGTGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTTTCTCTaa                                                                                                                      >  1:1148493/1‑140 (MQ=255)
                aTGGTTAAAGTGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTaa                                                                                                                      >  1:18869/1‑140 (MQ=255)
                aTGGTTAAAGCGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGCGGG‑TTTTTTTGTctctca                                                                                                                      >  2:827343/1‑138 (MQ=255)
                   gTTAAAGTGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGt                                                                                                                   <  1:672462/140‑1 (MQ=255)
                        aGTGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGa                                                                                                              <  1:1178690/140‑1 (MQ=255)
                             tGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTTTTTCTAACGCGGGGAAAAAt                                                                                                         >  2:329745/1‑140 (MQ=255)
                             tGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GG‑TTTTTTTTTCTCTAACGTGCGGAAAAAtt                                                                                                        >  1:250007/1‑140 (MQ=255)
                              ggCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTTTCTCTTAAGTGCGGaaaaaat                                                                                                        >  2:1253692/1‑138 (MQ=255)
                              ggCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAAtt                                                                                                        <  2:184630/140‑1 (MQ=255)
                                        tGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTTTCTCTAACGTGCGGaa                                                                                                             >  2:762513/1‑125 (MQ=255)
                                        tGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGaa                                                                                                             <  1:762513/125‑1 (MQ=255)
                                                ggAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTTTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACAtttt                                                                                      >  1:486558/1‑140 (MQ=255)
                                                  aaGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACAtttttt                                                                                    >  2:846609/1‑140 (MQ=255)
                                                   aGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATATCCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTg                                                                                   <  2:1092718/140‑1 (MQ=255)
                                                     ccGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTa                                                                                 <  1:901088/140‑1 (MQ=255)
                                                     ccGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTa                                                                                 <  1:550260/140‑1 (MQ=255)
                                                       gCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATTAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACa                                                                               <  2:1176474/140‑1 (MQ=255)
                                                       acagcTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACa                                                                               <  1:177445/136‑1 (MQ=255)
                                                            tATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGa                                                                          <  2:314981/140‑1 (MQ=255)
                                                              ttGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTTTCTTTTAAGCGCGGAAAAATTTTTTTCTCTTCACCTTTTTTTTATAACCGACa                                                                        >  2:598038/1‑140 (MQ=255)
                                                               tGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTAGCCTGAGGC‑GGTTTTTTTTTTCTCTAAAGTGCGGAAAAATTTTTTTCTCTTCACATTTTTTGTACAACCGACAt                                                                       >  2:1112419/1‑140 (MQ=255)
                                                                 cacaAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTTTCTCTAACGTGCGGGAAAATTTGTTCCTCTTCACATTTTTTTTACAACCCACATGc                                                                     >  2:222411/1‑140 (MQ=255)
                                                                 cacaAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGc                                                                     <  1:222411/140‑1 (MQ=255)
                                                                         aTAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTTTTTCTAAACTGCGGGAAAAATTGTTTCTCTTCCCATTTTTTTTTCAACCGACAAGCCCctgtgg                                                             >  2:858696/1‑138 (MQ=255)
                                                                            aaGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTc                                                          <  2:858528/140‑1 (MQ=255)
                                                                               gacagaCCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTcaca                                                       <  1:49462/135‑1 (MQ=255)
                                                                                 tCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTTTACAACCGACATGCCCGTGTAGCTcac                                                        >  1:1172972/1‑137 (MQ=255)
                                                                                 tCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTcac                                                        <  2:1172972/137‑1 (MQ=255)
                                                                                 tCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACaaa                                                     <  1:329745/140‑1 (MQ=255)
                                                                                 tCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACaaa                                                     <  2:188633/140‑1 (MQ=255)
                                                                                          aTTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTTTCTCTAACGTGCGGGAAAATTTTTTTCTCTTTACATTTTTTTTTCAACCGACATTCCCCTGTAGCTCACAAATATTAAAGt                                            >  2:924548/1‑140 (MQ=255)
                                                                                               aaaGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTTTTTCTAAAGTGCGGAAAAATTTTTTTCTCTTCACATTTTTTTTACAACCCACATGCCCCTGTAGCTCACAAATATGACAGtctgtt                                       >  2:49462/1‑135 (MQ=255)
                                                                                                  gATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACAAATATGACAGTGGCGTGaa                                    <  1:598038/140‑1 (MQ=255)
                                                                                                      tGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTTTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTTTACAACCGACATGCCCGTGTAGCTCACAAATATGACAGTGGCGTGAAtttt                                >  1:416938/1‑140 (MQ=255)
                                                                                                           atatAACCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACAAATATGACAGTGGCGTGAATTTTGCGCa                           <  2:486558/140‑1 (MQ=255)
                                                                                                                aCCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACAAATATGACAGTGGCGTGAATTTTGCGCATTGAc                      <  2:1134086/140‑1 (MQ=255)
                                                                                                                aCCGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACAAATATGACAGTGGCGTGAATTTTGCGCATTGAc                      <  1:846609/140‑1 (MQ=255)
                                                                                                                  cGTCTCCGGTATGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACAAATATGACAGTGGCGTGAATTTTGCGCATTGACgg                    <  2:692699/140‑1 (MQ=255)
                                                                                                                             tGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACAAATATGACAGTGGCGTGAATTTTGCGCATTGACGGCAGTTATGAtt         <  1:924548/140‑1 (MQ=255)
                                                                                                                             tGTTGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACAAATATGACAGTGGCGTGAATTTTGCGCATTGACGGCAGTTATGAtt         <  1:770133/140‑1 (MQ=255)
                                                                                                                               ttGCCTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACAAATATGACAGTGGCGTGAATTTTGCGCATTGACGGCAGTTATGATTcg       <  1:535825/140‑1 (MQ=255)
                                                                                                                                  ccTGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACAAATATGACAGTGGCGTGAATTTTGCGCATTGACGGCAGTTATGATTCGCgg    <  1:329410/140‑1 (MQ=255)
                                                                                                                                    tGAGGC‑GGTTTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACAAATATGACAGTGGCGTGAATTTTGCGCATTGACGGCAGTTATGATTCGCGGTa  <  1:635370/140‑1 (MQ=255)
                                                                                                                                             |                                                                                                                                   
GGATGGTTACGATGAGATGGTTAAAGTGCTGGCCGGTGTCTGGAGTCAGGAAGCCGCTTCTATTGCACAAGAGATAAAGCGTCTACCTTAATTATAAAGATTTGTAAATATAACCGTCTCCGGTATGTTGCCTGAGGC‑GG‑TTTTTTTGTCTCTAACGTGCGGAAAAATTTGTTCCTCTTCACATTTTTTGTACAACCGACATGCCCGTGTAGCTCACAAATATGACAGTGGCGTGAATTTTGCGCATTGACGGCAGTTATGATTCGCGGTA  >  NC_000913/1015369‑1015639

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A