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
A1 F52 I1 R1 27 78.9 1851050 96.3% 1782561 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 1,440,085 G→T intergenic (‑45/+126) cspA_2 ← / ← USA300TCH1516_01338 Cold shock protein CspA/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,440,0850GT98.4% 181.1 / NA 61intergenic (‑45/+126)cspA_2/USA300TCH1516_01338Cold shock protein CspA/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base T (26/34);  minor base A (0/1);  total (26/35)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTA  >  USA300TCH1516_ALE/1439950‑1440221
                                                                                                                                        |                                                                                                                                        
aaaaaTGTACGATTACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCatat                                                                                                                                     <  2:318269/141‑1 (MQ=255)
 aaaaTGTAGGAATCCGTCATTTTCTCCTTCAACTGCGATGAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATAtt                                                                                                                                    <  2:433458/141‑1 (MQ=255)
  aaaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTa                                                                                                                                   <  1:586130/141‑1 (MQ=255)
   aaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAc                                                                                                                                  <  1:189421/141‑1 (MQ=255)
     tGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaa                                                                                                                                >  2:276180/1‑141 (MQ=255)
      gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaa                                                                                                                               >  2:269183/1‑141 (MQ=255)
      gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCCTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaa                                                                                                                               >  1:605564/1‑141 (MQ=255)
       tACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaa                                                                                                                              <  1:68422/141‑1 (MQ=255)
             ttcGTCATTTTCTCCTTCAACTTCGGTAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTCCCTTGTTTCATAATCTGAATCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACa                                                                                                                        <  1:116579/139‑1 (MQ=255)
               cGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATg                                                                                                                      >  1:299685/1‑141 (MQ=255)
                gTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAGTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGc                                                                                                                     >  2:751041/1‑141 (MQ=255)
                     tttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAtt                                                                                                                <  1:581724/141‑1 (MQ=255)
                      ttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATACTTATTCTCAGATTACAAAAACTACATGCAAAttt                                                                                                               >  2:235215/1‑141 (MQ=255)
                         tcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAc                                                                                                            >  1:39728/1‑141 (MQ=255)
                          cattCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAGATTTCACt                                                                                                           <  2:850216/139‑1 (MQ=255)
                                aCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAata                                                                                                     <  1:788405/141‑1 (MQ=255)
                                    cGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCCCTCAAATATTCt                                                                                                 >  2:401795/1‑141 (MQ=255)
                                    cGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                                                                                                 <  2:254160/141‑1 (MQ=255)
                                     gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                                                                >  2:302932/1‑141 (MQ=255)
                                     gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                                                                <  1:604783/141‑1 (MQ=255)
                                     gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                                                                <  1:816194/141‑1 (MQ=255)
                                     gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                                                                <  1:816184/141‑1 (MQ=255)
                                             cgtaTCCTTTTTCAGCGTTAAAACATCTA‑ACTGTACCTTGTTTCATCATCAGACACCTCCAAGACTAACATTCATCCAATATGCTTATAAACAAAAAAAAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCCatat                                                                                        <  2:846601/138‑1 (MQ=255)
                                             cGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGAGTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCACATATTCTTTGCAatat                                                                                        <  2:667673/141‑1 (MQ=255)
                                                  ccTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTCAAATTCATTCAATATGCTTATTCTCATATTACAACAAATACATCCAAATTTCACTCCAATATTCTTTGCAATATGGcat                                                                                   >  1:732932/1‑141 (MQ=255)
                                                  ccTTGTTCATTGTTAAAATAATTA‑GCGGTCCCTCGTTTCATACTCTGAAACCTCCAAGCCTAAAATTCACTCCATACGTTTATTCTCTTATGACAAAAAATACATGCAGATTTCACTCAAATATTCTTTGCAAGAGGGagt                                                                                   <  2:863277/141‑3 (MQ=255)
                                                    tttttCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataa                                                                                 >  1:317692/1‑141 (MQ=255)
                                                    tttttCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataa                                                                                 <  2:745417/141‑1 (MQ=255)
                                                       ctCACCGTTAAACCATTTACAATG‑ACCATGTTGCATAATCTGAAACCTTCAAGACTAATATTCATTCAATATGCTTATTCTCCTATTACAAAAAATACATGCAACTTTCACTCAAATATTCTTTGCAATATGGAATAatca                                                                              <  1:855596/140‑1 (MQ=255)
                                                          aGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCACGACTAAAGTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCt                                                                           <  1:680521/141‑1 (MQ=255)
                                                             gTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCGGCt                                                                        >  1:62522/1‑141 (MQ=255)
                                                                 aaCCATTTA‑ACTGTTCCTTGTTCCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATTCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATCGAATAATCATCTGCTTAAc                                                                    <  2:620912/141‑1 (MQ=255)
                                                                     aTTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGt                                                                >  2:139791/1‑141 (MQ=255)
                                                                           aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattat                                                           >  1:42672/1‑141 (MQ=255)
                                                                               tACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAATCAAATATTCTTTGCAATATGGAATAATCATCTGCTTACCTTGTATTAGAGTg                                                       >  1:811841/1‑141 (MQ=255)
                                                                                  cTTGTTTCATCATCTGAAACCTCCAAGACTAGAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAg                                                    <  2:732932/141‑1 (MQ=255)
                                                                                    tGTTTCATAATCTGAAACCTCAAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtt                                                  <  2:482684/141‑1 (MQ=255)
                                                                                      tttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTGAACTTGTATTATAGTGCAGttat                                                >  1:337229/1‑141 (MQ=255)
                                                                                       ttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACGCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatt                                               <  2:86431/141‑1 (MQ=255)
                                                                                        tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatta                                              >  2:290930/1‑141 (MQ=255)
                                                                                        tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatta                                              >  2:585478/1‑141 (MQ=255)
                                                                                          aTAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTAcc                                            <  1:93790/141‑1 (MQ=255)
                                                                                               cTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAtt                                       <  2:299685/141‑1 (MQ=255)
                                                                                                             aCTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAataata                         >  1:189307/1‑141 (MQ=255)
                                                                                                              atAAAATTCATTCAATATGCTTATTCTCATAATACAAAAAATACATGCAAATTTCACTTAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTCTATCATAGTGCAGTTATTACCAAATTGCAATACAAtaataa                        <  2:606030/140‑1 (MQ=255)
                                                                                                                aaaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATGTGCATTGATCTTGGGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAGTAATaaaa                      >  1:212895/1‑141 (MQ=255)
                                                                                                                aaaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaa                      >  1:894267/1‑141 (MQ=255)
                                                                                                                aaaaCTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGATTAACTAGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaa                      <  2:604776/141‑1 (MQ=255)
                                                                                                                  aaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaaaa                    <  1:245442/141‑1 (MQ=255)
                                                                                                                       attcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAGTATTc               <  2:317692/141‑1 (MQ=255)
                                                                                                                       attcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTc               <  1:776722/141‑1 (MQ=255)
                                                                                                                          caATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATCCAATAATAAAAAATATTCGtt            >  1:352322/1‑141 (MQ=255)
                                                                                                                          caATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCAtt            <  1:139791/141‑1 (MQ=255)
                                                                                                                             tatGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTaa         >  1:75642/1‑141 (MQ=255)
                                                                                                                             tatGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTAAAATATTCTTTGCAATATGGAATAATCATCTGATTAACTTGTATTATAGTGCAGTTATTAACAAATTGCAATACAATAATAAAAAATATTCATTTaa         >  1:172431/1‑141 (MQ=255)
                                                                                                                                gCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAAGAATAAAAAATATTCATTTAATCa      >  2:836691/1‑141 (MQ=255)
                                                                                                                                   tATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatt   <  1:302932/141‑1 (MQ=255)
                                                                                                                                    tttCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatta  <  1:570220/140‑1 (MQ=255)
                                                                                                                                    aTTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatta  <  1:571438/141‑1 (MQ=255)
                                                                                                                                    aTTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatta  >  1:871002/1‑141 (MQ=255)
                                                                                                                                    aTTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatta  <  1:290930/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                        
AAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTA  >  USA300TCH1516_ALE/1439950‑1440221

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A