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
A9 F174 I0 R1 55 81.0 1740380 95.7% 1665543 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,440,085 G→T 100% intergenic (‑45/‑891) cspA ← / → xpaC cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,440,0850GT96.5% 161.9 / ‑4.9 57intergenic (‑45/‑891)cspA/xpaCcold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC
Reads supporting (aligned to +/- strand):  ref base G (1/0);  major base T (29/24);  minor base A (1/2);  total (31/26)
Fisher's exact test for biased strand distribution p-value = 5.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAAT  >  CP000730/1439950‑1440219
                                                                                                                                       |                                                                                                                                      
aaaaaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCatat                                                                                                                                   <  1:540264/141‑1 (MQ=255)
   aaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTaa                                                                                                                                >  2:236194/1‑140 (MQ=255)
    aTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACa                                                                                                                               <  2:111638/141‑1 (MQ=255)
    aTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACa                                                                                                                               >  2:752096/1‑141 (MQ=255)
      gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaa                                                                                                                             <  1:752096/141‑1 (MQ=255)
         cGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaaaa                                                                                                                          >  1:439889/1‑141 (MQ=255)
         cGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaaaa                                                                                                                          >  1:269274/1‑141 (MQ=255)
         cGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaaaa                                                                                                                          >  2:291626/1‑141 (MQ=255)
            aTACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATAc                                                                                                                       <  1:263553/141‑1 (MQ=255)
            aTACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCAGAAACCTCCAAGACTAAAATTCATTCAATATTCTTATTCTCATCTTACAAAAAATAc                                                                                                                       >  1:850365/1‑141 (MQ=255)
                gTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGc                                                                                                                   <  2:691603/141‑1 (MQ=255)
                gTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGc                                                                                                                   >  2:717608/1‑141 (MQ=255)
                gTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGATTTTTCATACATTACAAAAAATACATGc                                                                                                                   >  2:604489/1‑141 (MQ=255)
                 tCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAACAAAtacataca                                                                                                                  >  1:260303/1‑141 (MQ=255)
                              cAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaaa                                                                                                     <  2:30463/141‑1 (MQ=255)
                               aaCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTGTTCTCATATTACAAAAAATACATGCAAATTTCACTCAAat                                                                                                    <  2:562437/141‑1 (MQ=255)
                               aaCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAat                                                                                                    >  2:225054/1‑141 (MQ=255)
                                 cTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAatat                                                                                                  <  2:395576/141‑1 (MQ=255)
                                   tCGATAAAGCCGACTCCTTTTTCAGCGTTAAACCTGTTAACTGTACCTTGTTTCCTAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATCTTACAAAAAATACATGCAAATTTCAATCAAATAttt                                                                                                >  2:358056/1‑140 (MQ=255)
                                    cGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACAGCCAAATTTCACTCAAATATTCt                                                                                               <  1:860684/141‑1 (MQ=255)
                                          aGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTAATCTCATATTACAAAAAATAAATGCAAATTTCACTCAAATATTCTTTGCaa                                                                                         >  2:565425/1‑141 (MQ=255)
                                              gAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATg                                                                                     <  2:316742/141‑1 (MQ=255)
                                              gAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACAAAAATTCATTCAATATGCTTGTTCTCCTATTACAAAAAATACATGCAACTTTACCTCAAATATTCTTTGACATATg                                                                                     >  1:280745/1‑141 (MQ=255)
                                                        tCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat                                                                           <  1:381988/141‑1 (MQ=255)
                                                           tcGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTg                                                                        <  2:85417/140‑1 (MQ=255)
                                                              gtaacacATTTAACTGTACCTTGTTTCATAATCTGAAACCGCCAAGACGCAAATTAATTCAATATGCGTAGTCACATCTTACAAACAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCtt                                                                     <  2:384600/135‑1 (MQ=255)
                                                                aaaCCATTTAACTGTATCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTaa                                                                   >  1:378525/1‑141 (MQ=255)
                                                                aaaCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTaa                                                                   >  2:117109/1‑141 (MQ=255)
                                                                 aaCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAAc                                                                  >  1:828137/1‑141 (MQ=255)
                                                                  aCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACt                                                                 >  1:342122/1‑141 (MQ=255)
                                                                       ttcaCTGTACCTTGTTTCATAAACTCAAGTCGCCAAGACTCAAATTCATTCTATAGTCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtat                                                            <  2:787206/138‑1 (MQ=255)
                                                                       ttacctttcccTTGTTTCATAATCTGAAACCTCCAAGAATAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTGCTCTCAACTATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtat                                                            <  2:31913/132‑1 (MQ=255)
                                                                         aaCTGTACCTTGTTTCATAATCTGAAACCCCCCAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtatta                                                          <  1:236194/141‑1 (MQ=255)
                                                                          aCTGTACCTTGTTTCGTAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattat                                                         >  1:641724/1‑141 (MQ=255)
                                                                          aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattat                                                         >  1:621842/1‑141 (MQ=255)
                                                                          aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTAAAATATTCTTTGCAATATTGAATAATCATCTGCTTAACTTGtattat                                                         >  2:234040/1‑141 (MQ=255)
                                                                          aCTGTACCTTGTTTCAAAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattat                                                         >  1:428512/1‑141 (MQ=255)
                                                                             ttACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGt                                                      <  2:192261/140‑1 (MQ=255)
                                                                                ccTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCa                                                   <  1:604489/141‑1 (MQ=255)
                                                                                ccTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCa                                                   <  1:717608/141‑1 (MQ=255)
                                                                                   tGTTTAATAATCTGAAACCTCAAAAACTAAAATTCATTCAATATGCTTATTAAAAAAAAAAAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtt                                                <  2:314433/141‑1 (MQ=255)
                                                                                     tttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttat                                              <  1:783066/141‑1 (MQ=255)
                                                                                           aaTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCGGCTTAACTTGTATTATAGTGCAGTTATTACCaa                                        >  1:711722/1‑141 (MQ=255)
                                                                                              cTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAtt                                     >  1:130935/1‑141 (MQ=255)
                                                                                               tGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTg                                    >  2:367886/1‑141 (MQ=255)
                                                                                                gAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGc                                   <  2:408852/141‑1 (MQ=255)
                                                                                                     cTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATATTGCGGTTATTACAAAATTGcaataa                              >  2:626242/1‑140 (MQ=255)
                                                                                                             cTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAAtaataa                      <  1:394620/141‑1 (MQ=255)
                                                                                                              tAAAATTCATTCAATCTGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaa                     >  1:434350/1‑141 (MQ=255)
                                                                                                                aaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaaa                   <  2:849545/141‑1 (MQ=255)
                                                                                                                   tgcattcaATATGGTTATTCTCATATTACAAAAACTACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCGTAACTTGTATTATAGTGCAGTTATTCCCAAATTGCAATACAATAATaaaaaaca                <  2:731752/139‑3 (MQ=255)
                                                                                                                     cattcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATAtt              >  1:498697/1‑141 (MQ=255)
                                                                                                                     cattcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATAtt              >  1:634313/1‑141 (MQ=255)
                                                                                                                       ttcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCa            >  1:514225/1‑141 (MQ=255)
                                                                                                                              tGCATATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATc     <  1:499062/141‑1 (MQ=255)
                                                                                                                                cTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTATTTGCAATATGGAATAATAATCTGCTTAACTTGTATTCTAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTAATTTAATCaa   >  2:422001/1‑141 (MQ=255)
                                                                                                                                 ttATTCTCATATTACAACAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAat  >  2:525883/1‑141 (MQ=255)
                                                                                                                                       |                                                                                                                                      
AAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAAT  >  CP000730/1439950‑1440219

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A