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 3,101,039 (C)7→8 coding (585/720 nt) yggN ← DUF2884 family putative periplasmic protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,101,0321.C93.9% 160.1 / 2.6 49coding (592/720 nt)yggNDUF2884 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base . (0/3);  new base C (21/25);  total (21/28)
Fisher's exact test for biased strand distribution p-value = 2.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAG‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACTAATTGCTGGCCTTCGGCG  >  NC_000913/3100900‑3101165
                                                                                                                                      |                                                                                                                                     
agGATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAG‑cccccc                                                                                                                                 >  1:849882/1‑139 (MQ=255)
 ggATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAG‑ccccccc                                                                                                                                >  1:1529341/1‑139 (MQ=255)
    ttattTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCCG‑CCCCCCCAgg                                                                                                                             <  1:372992/139‑1 (MQ=255)
     tattTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAG‑ccccccccagg                                                                                                                            <  1:810404/139‑5 (MQ=255)
       ttttAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCt                                                                                                                           <  1:172972/139‑1 (MQ=255)
            aaTTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCa                                                                                                                      <  1:1498601/139‑1 (MQ=255)
            aaTTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAG‑ccccccccagg                                                                                                                            >  2:746944/1‑128 (MQ=255)
            aaTTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAG‑ccccccccagg                                                                                                                            <  1:746944/132‑5 (MQ=255)
               tCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGca                                                                                                                   <  2:871482/139‑1 (MQ=255)
               tCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGca                                                                                                                   <  2:1255652/139‑1 (MQ=255)
                 ccGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAG‑CCCCCCCAGGCTTCCCAGCACAt                                                                                                                <  1:111153/139‑1 (MQ=255)
                              tGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGt                                                                                                    >  2:754527/1‑139 (MQ=255)
                              tGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGt                                                                                                    >  1:770558/1‑139 (MQ=255)
                                   gttacctCCAAAGTCAAAACGCGGCTTAAAACCTCTTTTCCAAACCTCTTGAAATCTTTTTCCTGCTTTTTCCACTCCGTTTGGATTTGAGGTTGCCGG‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTAccg                                                                                               <  2:585404/133‑1 (MQ=255)
                                   cTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGGTTGCAG‑ccccccccagg                                                                                                                            >  1:1105822/1‑105 (MQ=255)
                                   cTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGGTTGCAG‑ccccccccagg                                                                                                                            <  2:1105822/109‑5 (MQ=255)
                                   cTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTAccg                                                                                               >  1:1458042/1‑139 (MQ=255)
                                                tCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCa                                                                                  >  2:283057/1‑139 (MQ=255)
                                                tCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCa                                                                                  >  1:1543063/1‑139 (MQ=255)
                                                  acaACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCAcc                                                                                >  1:618834/1‑139 (MQ=255)
                                                  acaACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAG‑c                                                                                                                                      <  2:736641/84‑1 (MQ=255)
                                                  acaACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAG‑c                                                                                                                                      >  1:736641/1‑84 (MQ=255)
                                                             aCAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGcc                                                                     <  2:1482723/139‑1 (MQ=255)
                                                               aaaCATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCa                                                                   <  1:1005945/139‑1 (MQ=255)
                                                                aaCATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt                                                                  <  1:754527/139‑1 (MQ=255)
                                                                     cTTTGCCAAACTGCTGGAAATCTTTTTCCTTCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCAt                                                             <  2:1543063/139‑1 (MQ=255)
                                                                     cTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCAt                                                             >  2:777083/1‑139 (MQ=255)
                                                                        tGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGc                                                                                                                    >  1:1206250/1‑81 (MQ=255)
                                                                        tGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGc                                                                                                                    <  2:1206250/81‑1 (MQ=255)
                                                                        tGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGt                                                                                                           >  2:147846/1‑90 (MQ=255)
                                                                        tGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGt                                                                                                           <  1:147846/90‑1 (MQ=255)
                                                                        tGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTaa                                                          >  2:569852/1‑139 (MQ=255)
                                                                          ccAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATg                                                        <  1:777083/139‑1 (MQ=255)
                                                                               ctgctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTc                                                   <  2:1458042/139‑1 (MQ=255)
                                                                               ctgctgGAAATCTTTTTCCCGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTc                                                   >  1:259908/1‑139 (MQ=255)
                                                                                  ctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTAccgccg                                                                                            >  2:1336799/1‑95 (MQ=255)
                                                                                  ctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTAccgccg                                                                                            <  1:1336799/95‑1 (MQ=255)
                                                                                  ctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTg                                                >  2:205508/1‑139 (MQ=255)
                                                                                    ggAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTa                                              <  1:569852/139‑1 (MQ=255)
                                                                                          cTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTc                                        <  1:1550437/139‑1 (MQ=255)
                                                                                            ttttCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATg                                                        >  1:829998/1‑121 (MQ=255)
                                                                                            ttttCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATg                                                        <  2:829998/121‑1 (MQ=255)
                                                                                            ttttCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCa                                      >  2:716860/1‑139 (MQ=255)
                                                                                                   gCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTg                               >  1:398140/1‑139 (MQ=255)
                                                                                                    cTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGc                              <  1:190722/139‑1 (MQ=255)
                                                                                                    cTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGc                              <  1:343223/139‑1 (MQ=255)
                                                                                                     tttttCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGcc                             <  1:283057/139‑1 (MQ=255)
                                                                                                         tCCACTCGGTTTGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGAt                         <  2:259908/139‑1 (MQ=255)
                                                                                                                  tttGGA‑TTGAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACTAAtt                >  2:1201961/1‑139 (MQ=255)
                                                                                                                           gAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGAt                         <  2:1321413/122‑1 (MQ=255)
                                                                                                                           gAGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGAt                         >  1:1321413/1‑122 (MQ=255)
                                                                                                                            aGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt                                                                  <  2:768716/80‑1 (MQ=255)
                                                                                                                            aGGATTGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt                                                                  >  1:768716/1‑80 (MQ=255)
                                                                                                                                 tGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCAc                                                                                 >  2:163806/1‑60 (MQ=255)
                                                                                                                                 tGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCAc                                                                                 <  1:163806/60‑1 (MQ=255)
                                                                                                                                 tGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATg                                                        >  2:355962/1‑85 (MQ=255)
                                                                                                                                 tGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATg                                                        <  1:355962/85‑1 (MQ=255)
                                                                                                                                 tGCAGCCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACTAATTGCTGGCCTTCGgcg  <  1:205508/139‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                     
AGGATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGA‑TTGAGGATTGCAG‑CCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACTAATTGCTGGCCTTCGGCG  >  NC_000913/3100900‑3101165

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A