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
A3 F50 I2 R1 193 39.9 1341687 91.8% 1231668 149.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,196,367 A→T D129E (GAT→GAA)  hldE ← heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,196,3670AT98.1% 194.2 / ‑3.1 52D129E (GAT→GAA) hldEheptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base T (24/27);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 4.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01

GATCAATCAGCACCGGAACACCCGCTTTACGCGCCAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGATCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATTTGACGTTGACGTCGGCCAGAGATTTACTCAGCG  >  NC_000913/3196222‑3196512
                                                                                                                                                 |                                                                                                                                                 
gATCAATCAGCACCGGAACACCCGCTTTACGCGCCAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCa                                                                                                                                                <  1:413279/149‑1 (MQ=255)
 atcaatcaGCACCGGAACACCCGCTTTACGCGCCAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAaca                                                                                                                                             <  1:601984/151‑1 (MQ=255)
  tcaatcaGCACCGGAACACCCGCTTTACGCGCCAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCACTCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAacac                                                                                                                                            >  1:508169/1‑151 (MQ=255)
  tcaatcaGCACCGGAACACCCGCTTTACGCGCCAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAacac                                                                                                                                            >  1:562803/1‑151 (MQ=255)
   caatcaGCACCGGAACACCCGCTTTACGCGCCAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACAcc                                                                                                                                           <  2:274334/151‑1 (MQ=255)
     atcaGCACCGGAACACCCGCTTTACGCGCCAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCtt                                                                                                                                         >  2:586306/1‑151 (MQ=255)
     atcaGCACCGGAACACCCGCTTTACGCGCCAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCtt                                                                                                                                         >  1:244696/1‑151 (MQ=255)
           aCCGGAACACCCGCTTTACGCGCCAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAAc                                                                                                                                   <  2:384523/151‑1 (MQ=255)
                    cccGCTTTACGCGCCAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCaa                                                                                                                          <  1:382273/151‑1 (MQ=255)
                               cgcCAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTAGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACgg                                                                                                               <  2:552693/151‑1 (MQ=255)
                                gcCAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACgg                                                                                                               >  2:535819/1‑150 (MQ=255)
                                 ccAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGAt                                                                                                             <  1:597884/151‑1 (MQ=255)
                                  cAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATc                                                                                                            >  2:258916/1‑151 (MQ=255)
                                  cAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATc                                                                                                            <  2:394019/151‑1 (MQ=255)
                                      tGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCt                                                                                                        >  2:379140/1‑151 (MQ=255)
                                        gATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTgt                                                                                                      >  1:653451/1‑151 (MQ=255)
                                         atcatcTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTgtt                                                                                                     >  2:384544/1‑151 (MQ=255)
                                         atcatcTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTgtt                                                                                                     <  2:159083/151‑1 (MQ=255)
                                          tcatcTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTgttg                                                                                                    >  1:648009/1‑151 (MQ=255)
                                           catcTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTgttg                                                                                                    <  1:5632/150‑1 (MQ=255)
                                                gctgTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGc                                                                                               <  1:402604/150‑1 (MQ=255)
                                                   gTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGa                                                                                           <  1:523645/151‑1 (MQ=255)
                                                   gTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGa                                                                                           <  1:378350/151‑1 (MQ=255)
                                                     aCGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGaaa                                                                                         <  1:76619/151‑1 (MQ=255)
                                                     aCGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGaa                                                                                          <  2:29098/150‑1 (MQ=255)
                                                           gCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTAcc                                                                                    <  1:258916/150‑1 (MQ=255)
                                                               gcgcACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTa                                                                                >  2:442220/1‑150 (MQ=255)
                                                                  cACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAAttt                                                                            <  2:658441/151‑1 (MQ=255)
                                                                  cACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGATCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAAttt                                                                            >  2:21892/1‑151 (MQ=255)
                                                                    ccTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTgg                                                                          <  1:482201/151‑1 (MQ=255)
                                                                         ggCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAAt                                                                      <  2:25858/150‑1 (MQ=255)
                                                                         ggCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATg                                                                     <  2:519318/151‑1 (MQ=255)
                                                                                   gAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCg                                                           >  1:522546/1‑151 (MQ=255)
                                                                                       gCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCgg                                                       <  1:639412/151‑1 (MQ=255)
                                                                                         aCCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGt                                                      >  2:94109/1‑150 (MQ=255)
                                                                                                cgcCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAAc                                              >  2:218303/1‑151 (MQ=255)
                                                                                                  ccAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGa                                            <  2:172413/151‑1 (MQ=255)
                                                                                                      tCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTc                                        >  1:241720/1‑151 (MQ=255)
                                                                                                        gAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGc                                      >  1:238981/1‑151 (MQ=255)
                                                                                                            tCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCAttt                                  >  2:137004/1‑151 (MQ=255)
                                                                                                              aGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATttg                                 >  2:523400/1‑150 (MQ=255)
                                                                                                               gcgcCTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATttgac                               >  1:158725/1‑151 (MQ=255)
                                                                                                                   cTGATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATttgacgttg                           >  1:393698/1‑151 (MQ=255)
                                                                                                                     gATTAATCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATttgacgttg                           <  1:137000/149‑1 (MQ=255)
                                                                                                                          aTCCGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATTTGACGTTGACGTCgg                    >  2:209365/1‑151 (MQ=255)
                                                                                                                             cGCTCGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATTTGACGTTGACGTCGGcc                  >  2:55663/1‑150 (MQ=255)
                                                                                                                                 cGTGCAGCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATTTGACGTTGACGTCGGCCagag              <  2:120344/150‑1 (MQ=255)
                                                                                                                                       gCGGCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATTTGACGTTGACGTCGGCCAGAGATTTACt       <  2:158728/151‑1 (MQ=255)
                                                                                                                                          gCTGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATTTGACGTTGACGTCGGCCAGAGATTTACTCAg    <  1:384540/151‑1 (MQ=255)
                                                                                                                                            tGCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATTTGACGTTGACGTCGGCCAGAGATTTACTCAgcg  >  1:113014/1‑151 (MQ=255)
                                                                                                                                             gCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATTTGACGTTGACGTCGGCCAGAGAt            >  1:84600/1‑140 (MQ=255)
                                                                                                                                             gCGGTTCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATTTGACGTTGACGTCGGCCAGAGAt            <  2:84601/140‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                 
GATCAATCAGCACCGGAACACCCGCTTTACGCGCCAGTTGGATCATCTGCTGTACGCTTGCCAGCGCACCTTTGGCGTAGTCAGAAAGCACCAGCGCGCCAATCGAACTCAGCGCCTGATTAATCCGCTCGTGCAGCGGCTGCGGATCAACACCTTCGAAACCTTCTTCAAAATCCAGACGGATCAGCTGTTGGTTGCGGGAAAGTACCCGTAATTTGGTAATGGTCGGATGCGTCGGTACAGAAACGAAGTCGCATTTGACGTTGACGTCGGCCAGAGATTTACTCAGCG  >  NC_000913/3196222‑3196512

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A