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
A12 F56 I0 R1 312 170.3 8276235 93.7% 7754832 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,642,062:1 +T 100% coding (208/213 nt) cspF → Qin prophage; cold shock protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,642,0591.T57.4% 134.5 / 113.1 68coding (205/213 nt)cspFQin prophage; cold shock protein
Reads supporting (aligned to +/- strand):  ref base . (16/13);  new base T (18/21);  total (34/34)
Fisher's exact test for biased strand distribution p-value = 6.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCTCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGACTGGTTGATTG  >  NC_000913/1641961‑1642158
                                                                                                   |                                                                                                    
cgcTCAATCTCCGCGACGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t                                                                                                     <  2:2418331/100‑1 (MQ=255)
 gcTCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑t                                                                                                   <  1:589738/100‑1 (MQ=255)
 gcTCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑t                                                                                                   >  1:3599138/1‑100 (MQ=255)
   tCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTc                                                                                                 <  1:1423232/100‑1 (MQ=255)
     aaTCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑tttca                                                                                               <  2:2965907/100‑4 (MQ=255)
      aTCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑tttcat                                                                                              <  2:350506/100‑5 (MQ=255)
      aTCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑t‑tttcat                                                                                              >  1:2689006/1‑96 (MQ=255)
      aTCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATg                                                                                              <  2:2921116/100‑1 (MQ=255)
      aTCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACA‑t‑tttcat                                                                                              >  2:4000845/1‑96 (MQ=255)
         tcCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGc                                                                                           >  2:2545864/1‑100 (MQ=255)
          ccGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGc                                                                                           >  1:3331814/1‑100 (MQ=255)
          ccGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCt                                                                                          <  1:2667844/100‑1 (MQ=255)
           cgcgATGTAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGTCGGATAAATGGTCTGCGTGGCCCTTCAGTTGCCAATGTTTACC‑t‑tttcat                                                                                              <  2:511549/95‑5 (MQ=255)
                 gCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTaa                                                                                   <  1:1647797/100‑1 (MQ=255)
                   agaagaAATTACCACCGGATTCCGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAg                                                                                 >  2:2613872/1‑100 (MQ=255)
                   agaagaAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAAGGTTTACC‑T‑TTCATGAGCTATATTAAAg                                                                                 >  2:1170138/1‑100 (MQ=255)
                      agaaATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCtt                                                                              >  2:2915232/1‑100 (MQ=255)
                        aaaTTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTa                                                                            <  2:3643684/100‑1 (MQ=255)
                        aaaTTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTa                                                                            <  1:1097543/100‑1 (MQ=255)
                         aaTTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTa                                                                            >  2:656110/1‑100 (MQ=255)
                          aTTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAAt                                                                          <  2:3009331/100‑1 (MQ=255)
                              ccaccGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTc                                                                       >  1:2526674/1‑100 (MQ=255)
                              ccaccGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTc                                                                       >  1:1939563/1‑100 (MQ=255)
                              ccaccGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCa                                                                      >  1:2454004/1‑100 (MQ=255)
                                accGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAg                                                                     >  1:2240592/1‑100 (MQ=255)
                                 ccGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAgg                                                                    <  2:707106/100‑1 (MQ=255)
                                  cGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGc                                                                   <  2:1324274/100‑1 (MQ=255)
                                   ggATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGcc                                                                  <  1:1457856/100‑1 (MQ=255)
                                   ggATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGcc                                                                  >  1:1862834/1‑100 (MQ=255)
                                   ggATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGcc                                                                  >  1:2615605/1‑100 (MQ=255)
                                   ggATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGccc                                                                 >  1:1479561/1‑100 (MQ=255)
                                        aCGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATc                                                             >  1:2503402/1‑100 (MQ=255)
                                          gcgTGTAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATc                                                             <  1:19648/98‑1 (MQ=255)
                                          gcgTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCgg                                                           >  1:3277300/1‑100 (MQ=255)
                                             tGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGa                                                          <  2:3743070/98‑1 (MQ=255)
                                             tGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATc                                                        <  2:3137456/100‑1 (MQ=255)
                                             tGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATca                                                       >  1:3764707/1‑100 (MQ=255)
                                              ggAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATc                                                        <  2:3793874/99‑1 (MQ=255)
                                               gAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATcac                                                      <  1:2698638/100‑1 (MQ=255)
                                                 aTTTTGCTGGATAAATGGTCTGCGTGGCCCTTCCGCTGCCAATGTTTGCC‑T‑TTCATGAGCTATATTATAGCTTGAATGGCAGGCCCCAACGGATcac                                                      <  2:2705901/97‑1 (MQ=255)
                                                 aTTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATcacaca                                                   >  1:651069/1‑100 (MQ=255)
                                                      gCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGgag                                              >  1:362639/1‑100 (MQ=255)
                                                      gCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGgag                                              <  1:3920569/100‑1 (MQ=255)
                                                       ccGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGgaga                                             >  1:2585588/1‑100 (MQ=255)
                                                          gATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGt                                           <  2:3568830/100‑1 (MQ=255)
                                                            tAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGttt                                         <  1:662632/100‑1 (MQ=255)
                                                               aTGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCATGCCCCATCGGATCACACATGGAGAGTTTTTa                                      <  1:768197/100‑1 (MQ=255)
                                                               aTGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTAt                                     <  1:3391758/100‑1 (MQ=255)
                                                                tGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTGAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTAt                                     <  2:3050136/100‑1 (MQ=255)
                                                                tGGTCTGCGTGGCCCTTCAGCTGCCAATGTGTACCTT‑TTCATGAGCTATAATAAAGCTTTAATTTCAGGCCCCATCGGCTCACACACGGAGAGTTTTTAt                                     <  2:4083437/100‑1 (MQ=255)
                                                                 ggTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATg                                    <  1:3388500/100‑1 (MQ=255)
                                                                 ggTCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATg                                    <  1:2701803/100‑1 (MQ=255)
                                                                  atCTGCGTGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGa                                   >  2:3376388/2‑100 (MQ=255)
                                                                       cGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAAcc                             <  2:1489795/100‑1 (MQ=255)
                                                                         tGGCCCTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAAccc                            <  2:2503388/100‑1 (MQ=255)
                                                                            cacatCAGCAGCCAAAATTTACG‑TATTCATGAGCAATATTGAAGCTATAATGTCAAGCCCCATAGGGTCAGAGATGGAGAGTTTTTATGAAGAAcggcg                          >  2:2404281/5‑95 (MQ=255)
                                                                             ccTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCgtc                        >  1:122092/1‑100 (MQ=255)
                                                                             ccTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCgtc                        >  2:1647737/1‑100 (MQ=255)
                                                                             ccTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCgtc                        <  1:3872319/100‑1 (MQ=255)
                                                                              cTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCgtct                       <  1:1954724/100‑1 (MQ=255)
                                                                              cTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCgtct                       >  1:3274452/1‑100 (MQ=255)
                                                                              cTTCAGCTGCCAATGTTTACCTT‑TTCATGAGCTATATGAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCgtct                       >  2:344239/1‑100 (MQ=255)
                                                                                  aGCTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCgtctgtct                   >  1:1711524/1‑100 (MQ=255)
                                                                                   gCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGTATAACCCCGTCTGTCTtg                 <  2:3876062/100‑1 (MQ=255)
                                                                                    cTGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTtg                 <  1:1496758/100‑1 (MQ=255)
                                                                                    cTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTtga                >  2:3379798/1‑100 (MQ=255)
                                                                                     tGCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTtga                <  2:1504300/100‑1 (MQ=255)
                                                                                      gCCAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTtgat               >  2:3571806/1‑100 (MQ=255)
                                                                                      gCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCACTCCTCATCGCATCACACATGTAGTGTTTTTATGACTACACCCgtct                       >  2:3584031/1‑91 (MQ=255)
                                                                                       ccAATGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTtgatg              >  2:1875428/1‑100 (MQ=255)
                                                                                       ccAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTtgatga             >  1:602952/1‑100 (MQ=255)
                                                                                        cAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGAc            >  2:1135947/1‑100 (MQ=255)
                                                                                         aaTGTTTACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGAc            >  2:1722297/1‑100 (MQ=255)
                                                                                            gTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGACTGGt        >  2:386373/1‑100 (MQ=255)
                                                                                              ttACCTT‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGACTGGtt       <  2:3042489/100‑1 (MQ=255)
                                                                                              ttACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGACTGGTTg      <  2:3698244/100‑1 (MQ=255)
                                                                                                  c‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGACTGGTTGATTg  >  1:4022771/1‑100 (MQ=255)
                                                                                                   |                                                                                                    
CGCTCAATCTCCGCGATGCAGAAGAAATTACCACCGGATTACGCGTGGAATTTTGCCGGATAAATGGTCTGCGTGGCCCTTCAGCTGCCAATGTTTACC‑T‑TTCATGAGCTATATTAAAGCTTTAATTTCAGGCCCCATCGGATCACACATGGAGAGTTTTTATGAATAACCCCGTCTGTCTTGATGACTGGTTGATTG  >  NC_000913/1641961‑1642158

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A