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
A2 F13 I0 R1 203 85.6 3649704 98.8% 3605907 146.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 2,051,065 T→G 26.1% intergenic (‑63/+23) PP_1825 ← / ← PP_1826 hypothetical protein/isochorismatase family hydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC2,051,0650TG26.1% 93.1 / 6.0 48intergenic (‑63/+23)PP_1825/PP_1826hypothetical protein/isochorismatase family hydrolase
Reads supporting (aligned to +/- strand):  ref base T (10/25);  new base G (10/3);  total (20/28)
Fisher's exact test for biased strand distribution p-value = 3.68e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGGCCGCCAGGCGGGCGCCCCAGTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGCCGTCCTTGAATGCCAGGTCACGGGTGG  >  NC_002947_CJ‑RC/2050923‑2051206
                                                                                                                                               |                                                                                                                                             
ccggccgCCAGGCGGGCGCCCCAGTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCTTTCCGCTCTCCTCGGTGGATATCCGGATTTCGACCTGCTTCTGCCCATCGGGTT‑CCGCCCGGCTGCCggg                                                                                                                                         <  1:95755/149‑1 (MQ=255)
   gccgccAGGCGGGCGCCCCAGTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCgg                                                                                                                                      <  7:463063/149‑1 (MQ=255)
   gccgccAGGCGGGCGCCCCAGTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCCCCCCGCGGCCcggcgg                                                                                                                                      >  4:47339/1‑149 (MQ=255)
      gccAGGCGGGCGCCCCAGTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTTCCCGCCCGCCGGCCgggggggg                                                                                                                                    >  5:66083/1‑147 (MQ=255)
           gcgggcgCCCCAGTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCaa                                                                                                                              <  3:221038/149‑1 (MQ=255)
              ggcgCCCCAGTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGcc                                                                                                                           >  2:272333/1‑149 (MQ=255)
                   cccAGTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCa                                                                                                                      >  7:379108/1‑149 (MQ=255)
                   cccAGTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCa                                                                                                                      <  6:99789/149‑1 (MQ=255)
                   cccAGTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCGGCCGGGCGGGGCGGCAAGCCGcg                                                                                                                        >  1:160637/1‑146 (MQ=255)
                   cccAGTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCCGCTGCCGGGCGGTCCTGCAAGCCGCt                                                                                                                        >  5:401891/1‑147 (MQ=255)
                     cAGTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCCGCTGCCGGGCGGTCCTGCAAGCCCCGCAg                                                                                                                     >  6:401639/1‑148 (MQ=255)
                       gTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGAt                                                                                                                   >  2:247816/1‑148 (MQ=255)
                          aCGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCCCCCCGCTGCCCGGCGGTCCGGCAAGCCCCGCCGATCAgg                                                                                                               >  8:20570/1‑149 (MQ=255)
                             cgGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGGTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTg                                                                                                            <  5:52043/149‑1 (MQ=255)
                               gTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGc                                                                                                          <  8:362032/149‑1 (MQ=255)
                                ttCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCg                                                                                                         <  2:191481/149‑1 (MQ=255)
                                      cgGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGTGGTgggg                                                                                                   <  8:407113/149‑1 (MQ=255)
                                             aGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGGTCTCCTGGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGc                                                                                            <  4:352188/149‑1 (MQ=255)
                                               gcgcTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCaa                                                                                          <  6:62938/149‑1 (MQ=255)
                                                 gcTTGGCGTCGAAACTCCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGACCATCGGGTT‑CCCCCCCGCGGCCCGGGGGTGCTCCAAACCACTAACATCAGGCTGGCGGTGCGGGCCACCCAAGc                                                                                        >  8:116996/1‑149 (MQ=255)
                                                     ggCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGaa                                                                                     <  7:217302/148‑1 (MQ=255)
                                                      gCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAg                                                                                    <  1:314980/148‑1 (MQ=255)
                                                             aaCTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAg                                                                             <  8:379108/148‑1 (MQ=255)
                                                                 gCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCGGCCGGGCGGTCCAGCAAGCCGCTCACATCAGGCAGGCGGTGGGGGCCACGCAAGACAAGTTGTAATCCAt                                                                         >  2:241458/1‑148 (MQ=255)
                                                                   cTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCAc                                                                      <  4:104354/149‑1 (MQ=255)
                                                                        aGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCCGCCCATCGGGTT‑CCGCCCCGCGGCCGGGCGGTGCTGGAAGCCGCGCAGATAAGGCTGGGGGGGGGGGCCCCCCAAGCGAAGTTTTGAGCCATCACGGcc                                                                  >  1:157562/1‑148 (MQ=255)
                                                                                  cGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTg                                                       <  7:116315/149‑1 (MQ=255)
                                                                                            ggTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTgc                                             <  5:401639/149‑1 (MQ=255)
                                                                                                gATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCCCCCCGCGGCCCGGGGGTGCGGCAAGCCCCGCAGAAAAGGCTGGGCGGGGGGGCCCCGCCAGCGAAGTTGTCAGCCAACACCGCCATTTAGCCCGGGTGAATATgcgccg                                         >  6:77520/1‑147 (MQ=255)
                                                                                                  tatCCGGAATTCGCCCTGCTGCGGCCCATCGGGTT‑CCGCGCGGCGGCCGGGGGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGc                                        <  1:232822/148‑1 (MQ=255)
                                                                                                    tCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑GCCCCCCGCGGCCCGGCGGGCCTGAAAAACCCGCAAATAAAGCTGGCGGGGGGGGGCCCCCAACCGAAAATTTCAACCATAACAGCCAAATATCACATGTGAATCATCGCGGccc                                      >  4:198515/1‑147 (MQ=255)
                                                                                                      cGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCCCCCCGCGGCCGGGCGGGGCGGCCAGCCCCGCAGAAACGGCGGGCGGGGGGGGGCCCCCCAGCGAACTTGTAAGCCCAAACCGCCAATTAGCACACGGGAAACAGCGCGGCCCGaa                                   >  4:437522/1‑149 (MQ=255)
                                                                                                       ggAATTCGACCTGCTGCTGCCCATCGGGTT‑GCGCCCCGCGGCCGGGGGGGGGGGCCACCCGCGCAGGTGACGCAGGGGGGGGGGGGCCCCCCAGCGAAGTTGTGAGCCCAGCCGGCCAGATATGCCAGGTGAATATGCGCGGcccgcat                                  >  6:3232/1‑144 (MQ=255)
                                                                                                              gACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGcc                            <  3:274220/148‑1 (MQ=255)
                                                                                                              gACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGcc                            <  8:228232/148‑1 (MQ=255)
                                                                                                                    ctgctgcCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGCCGTCCtt                      <  8:256370/148‑1 (MQ=255)
                                                                                                                    cggctgcCCAGCGGGTG‑CCGCCGGGCGGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGCCGTCCtt                      <  3:47339/146‑1 (MQ=255)
                                                                                                                       ctgcCCATCGGGTT‑CCGCCGGGGTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGATGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGCCGTCCTTGa                    <  6:66083/147‑1 (MQ=255)
                                                                                                                           ccATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGCCGTCCTTGAATGCCa              <  2:160637/149‑1 (MQ=255)
                                                                                                                                   tt‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGCCGTCCTTGAATGCCAGGTCACgg      <  6:419734/149‑1 (MQ=255)
                                                                                                                                    tgccGCCCGGCGGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGCCGTCCTTGAATGCCAGGTCACgg      <  3:276050/147‑1 (MQ=255)
                                                                                                                                    gcccgccgGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGCCGTCCTTGAATGCCAGGTCACgg      <  3:282139/147‑1 (MQ=255)
                                                                                                                                        gCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTgg                                                      <  6:226317/97‑1 (MQ=255)
                                                                                                                                        gCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTgg                                                      >  5:226317/1‑97 (MQ=255)
                                                                                                                                        gCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGCCGTCCTTGAATGCCAGGTCACGGGTgg  >  8:443564/1‑149 (MQ=255)
                                                                                                                                        gCCAGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGCCGTCCTTGAATGCCAGGTCACGGGTgg  >  4:115603/1‑149 (MQ=255)
                                                                                                                                          ccGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGCCGTCCtt                      <  2:199809/127‑1 (MQ=255)
                                                                                                                                          ccGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGCCGTCCtt                      >  1:199809/1‑127 (MQ=255)
                                                                                                                                               |                                                                                                                                             
CCGGCCGCCAGGCGGGCGCCCCAGTTACGCGGTTCGCGCGGGCGCAGGCGCTTGGCGTCGAAACTGCCTTTAAGCTTCATTCCGCTCTCCTCGGTGGATATCCGGAATTCGACCTGCTGCTGCCCATCGGGTT‑CCGCCCGGCTGCCGGGCGGTCCTGCAAGCCGCTCAGATCAGGCTGGCGGTGGGGGCCACGCAAGCGAAGTTGTCAGCCATCACGGCCATTTCGCACTGGTGAATCTGCGCGGCCGGAATGACGCCGTCCTTGAATGCCAGGTCACGGGTGG  >  NC_002947_CJ‑RC/2050923‑2051206

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A