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 F191 I0 R1 49 68.0 1456600 97.2% 1415815 140.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,386,119 G→A 62.5% P114L (CCG→CTG)  USA300HOU_2245 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,386,1190GA62.5% 35.2 / 55.3 61P114L (CCG→CTG) USA300HOU_2245hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (13/9);  new base A (17/20);  total (30/31)
Fisher's exact test for biased strand distribution p-value = 4.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.30e-01

TTTTTAGTACGCATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACTCC  >  CP000730/2385981‑2386249
                                                                                                                                          |                                                                                                                                  
tttttAGTACGCATGGAATCACTTTCTTCCCATTGGATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCgg                                                                                                                                   <  1:515444/140‑1 (MQ=255)
        aCGCATGGAATCACTTTCTTCCAATTTAATTAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCctacta                                                                                                                           <  2:149623/140‑1 (MQ=255)
           cATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACtt                                                                                                                        <  1:603669/140‑1 (MQ=255)
             tGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCa                                                                                                                      >  2:721711/1‑140 (MQ=255)
              ggAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCaa                                                                                                                     <  1:698527/140‑1 (MQ=255)
                aaTCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAAcc                                                                                                                   >  1:196856/1‑140 (MQ=255)
                 aTCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCt                                                                                                                  <  1:110167/140‑1 (MQ=255)
                  tCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTg                                                                                                                 >  1:59883/1‑140 (MQ=255)
                             ccATTGAATAAACAATGGTTGCGTCATTTCATCATCATCCTGATTCATTATATAAAGCAATCGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTa                                                                                                      <  1:14272/140‑1 (MQ=255)
                             ccATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTa                                                                                                      <  1:207271/140‑1 (MQ=255)
                              cATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAg                                                                                                     >  1:34676/1‑140 (MQ=255)
                                ttGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATTTAAAGCAATTGCCATTTTACCTTACCATTTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGtt                                                                                                   <  1:265136/140‑1 (MQ=255)
                                ttGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGtt                                                                                                   <  2:532890/140‑1 (MQ=255)
                                ttGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGtt                                                                                                   <  1:362782/140‑1 (MQ=255)
                                 tGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATCAATTATATAAAGAAATTGCCACTTTACCTTACCATCTTTATGTGTATCGCTTTCCCATTGACTCGGCCCTACTACTTCAACCTGCTCACCATGTAGttt                                                                                                  >  2:312413/1‑140 (MQ=255)
                                  gAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTa                                                                                                 >  2:539296/1‑140 (MQ=255)
                                      aaaaaaTGTCGCCTTACTTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATCTGTACCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAtttt                                                                                             <  1:591305/140‑1 (MQ=255)
                                      aaaaaaTGGTGGCTTAATTTCATCATCATCCTTATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCCTTTTAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAtttt                                                                                             <  2:119347/140‑1 (MQ=255)
                                      aaaaaaTGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAtttt                                                                                             <  1:668806/140‑1 (MQ=255)
                                      aaaaaaTGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAtttt                                                                                             <  2:544035/140‑1 (MQ=255)
                                       aaaaaTGGTGGCTTAATTTCATCATCCTCCTTGTTCATTATATAAAGCACTTGCCACTTTACCTTACCCTCTTTATGTGTAGCTCTTTCCATTTGAATCTTCCCTACTACTTCCAGCTGGTCACTTTTTAGTTTAttttt                                                                                            <  2:397782/140‑1 (MQ=255)
                                       aaaaaTGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAttttt                                                                                            <  2:656568/140‑1 (MQ=255)
                                       aaaaaTGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAttttt                                                                                            <  1:229955/140‑1 (MQ=255)
                                           aTGGTGGCTTAATTTCCTCATGATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACt                                                                                        >  1:372401/1‑140 (MQ=255)
                                               tggCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGACCTACTACTTCAAGCTGCTCACTTTGTAGTTTATATTTGACTACct                                                                                    >  1:494047/1‑140 (MQ=255)
                                                  cTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCCCTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCGCTTTGTAGTTTATTTTTTACTGCCTCta                                                                                 >  2:63955/1‑140 (MQ=255)
                                                          catcatcatCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCAttt                                                                         <  1:651971/140‑1 (MQ=255)
                                                          catcatcatCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCAttt                                                                         <  2:196856/140‑1 (MQ=255)
                                                            tcatcatcCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCATCTATATAATTTGt                                                                       >  1:323319/1‑140 (MQ=255)
                                                                catcCTGATTCATTATATAAAGCAATTGCCACTTTATATGACCATCTTTATGTGGAGCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGc                                                                   >  1:716959/1‑140 (MQ=255)
                                                                   ccTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTTAATCAGCCCTACTACTTCAACCTACTCACTTTGTAGTTTCTTTTTAACTGCCTCTATATCCTTTTTACGccaa                                                                >  2:659738/1‑140 (MQ=255)
                                                                     tGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTGGTACGcaaaca                                                              >  1:693217/1‑140 (MQ=255)
                                                                            ttATTTAAAGCAATTGCCACTTTACCTTAGCGTCTTTATGTGTATCTTTTTCCATTTGAATCAGTCCTACTACTTCAACATGCTCACTTTGTAGTTTATTTTTAACTGACTCTACATCATTTGTACGCAAACAAATAttt                                                       <  2:347523/140‑1 (MQ=255)
                                                                            ttATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATAttt                                                       >  1:623796/1‑140 (MQ=255)
                                                                            ttATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATAttt                                                       >  1:246115/1‑140 (MQ=255)
                                                                              atataAAGCAATTGCGACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATAttttt                                                     >  1:541300/1‑140 (MQ=255)
                                                                              atataAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATAttttt                                                     <  1:50884/140‑1 (MQ=255)
                                                                                ataAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTaa                                                   <  1:117524/140‑1 (MQ=255)
                                                                                   aaGCAATTTCCCCTTTACCTTACCATCTTTATGTGTATCTCTTTTCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGc                                                <  1:61353/140‑1 (MQ=255)
                                                                                         ttGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCt                                          >  1:124010/1‑140 (MQ=255)
                                                                                          tGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTc                                         <  1:54910/140‑1 (MQ=255)
                                                                                            ccACTTTTCCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCAt                                       <  2:176066/140‑1 (MQ=255)
                                                                                            ccACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTTTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCAt                                       >  1:67947/1‑140 (MQ=255)
                                                                                            ccACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATAATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCAt                                       >  1:668229/1‑140 (MQ=255)
                                                                                            ccACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCAt                                       <  2:681577/140‑1 (MQ=255)
                                                                                              aCTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCCTTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATAc                                     >  1:97754/1‑140 (MQ=255)
                                                                                              aCTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATAc                                     >  1:312177/1‑140 (MQ=255)
                                                                                               cTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACt                                    >  2:574855/1‑140 (MQ=255)
                                                                                                    ccttaccATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTctct                               >  2:517515/1‑140 (MQ=255)
                                                                                                    ccttaccATCTTTATGTGTATCTCTTTCCATTTGAAGCAGCCCTACTACATCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTctct                               >  2:81985/1‑140 (MQ=255)
                                                                                                     cttaccATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCtt                              >  1:219288/1‑140 (MQ=255)
                                                                                                            tCTGTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGATCACTTCGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATCTTTAAAGCCTTGCTCATACTTCTCTTGAACAAt                       <  2:479895/140‑1 (MQ=255)
                                                                                                                    tgtCTCTCTTTCCCTTTGAATCACACCTTCTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCTTTTATATCATTTGTACGCAAACAAATATTTTTAAAGCATTTGCAGTAGTTCTCTTGAACAATTTGAGTAg               <  2:155192/140‑1 (MQ=255)
                                                                                                                     gtATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTTCTCATTTTGTATTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGc              <  1:558719/140‑1 (MQ=255)
                                                                                                                      tATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTCTTTTTAACTGCCTCTATATCATTTGTACGCCAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGGAGCa             >  2:453983/1‑140 (MQ=255)
                                                                                                                          tctTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAg         <  2:34676/140‑1 (MQ=255)
                                                                                                                           ctTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAACGCCTTGCTCATACTTCTCTTGAACAATTTGCGTCGCACAAGc        >  2:284309/1‑140 (MQ=255)
                                                                                                                           ctTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGc        >  1:484649/1‑140 (MQ=255)
                                                                                                                           ctTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGATCATACTTCTCTTTAACAATTTGAGTAGCAAAAgt        >  1:126993/1‑139 (MQ=255)
                                                                                                                              tCCATTTGCATCTGCCCCACTACTTCAACCTTCTTACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAATAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGAc     <  1:37112/140‑1 (MQ=255)
                                                                                                                              tCCATTTGAATCGGCCCTACTTCTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGAc     <  2:586557/140‑1 (MQ=255)
                                                                                                                                 aTTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGATTcc  >  1:522331/1‑140 (MQ=255)
                                                                                                                                          |                                                                                                                                  
TTTTTAGTACGCATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCATCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACTCC  >  CP000730/2385981‑2386249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A