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
A2 F28 I1 R1 155 60.3 2039550 99.3% 2025273 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,417,546 (T)8→7 coding (218/276 nt) racC ← Rac prophage; protein RacC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,417,5390T.96.5% 221.8 / 2.9 57coding (225/276 nt)racCRac prophage; protein RacC
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base . (27/28);  total (28/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.32e-01

ATTAAAATTCGTTTTGTTCAGTGAATGATCTTGCCGGATACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGCTTTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACCACAGTGAATGGGGTTTCTTTATTTTCTGTTTTA  >  NC_000913/1417408‑1417674
                                                                                                                                   |                                                                                                                                       
aTTAAAATTCGTTTTGTTCAGTGAATGATCTTGCCGGATACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGCtttttttct                                                                                                                                 <  1:980270/140‑3 (MQ=255)
aTTAAAATTCGTTTTGTTCAGTGAATGATCTTGCCGGATACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGCtttttttct                                                                                                                                 >  1:337526/1‑138 (MQ=255)
aTTAAAATTCGTTTTGTTCAGTGAATGATCTTGCCGGATACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGCtttttttct                                                                                                                                 >  2:668745/1‑138 (MQ=255)
          gTTTTGTTCAGTGAATGATCTTGCCGGATACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGAt                                                                                                                      <  2:905340/140‑1 (MQ=255)
          gTTTTGTTCAGTGAATGATCTTGCCGGATACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCCTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGAt                                                                                                                      >  2:441601/1‑140 (MQ=255)
               gTTCAGTGAATGATCTTGCCGCATACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCttt                                                                                                                 <  2:926261/140‑1 (MQ=255)
                          gATCTTGCCGGATACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGAt                                                                                                                      >  1:1000327/1‑124 (MQ=255)
                          gATCTTGCCGGATACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGAt                                                                                                                      <  2:1000327/124‑1 (MQ=255)
                              ttGCCGGATACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAgg                                                                                                  <  2:337526/140‑1 (MQ=255)
                               tGCCGGATACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGc                                                                                                 >  2:222801/1‑140 (MQ=255)
                               tGCCGGATACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGc                                                                                                 >  1:68796/1‑140 (MQ=255)
                                      tACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACAtttt                                                                                          >  1:773900/1‑140 (MQ=255)
                                           acTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGa                                                                                     >  2:660204/1‑140 (MQ=255)
                                           acTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGa                                                                                     >  1:656901/1‑140 (MQ=255)
                                             tGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGaca                                                                                   <  2:656901/140‑1 (MQ=255)
                                               ttCATAGCCTGCGCCATACGCAGGTTATTTCTTTCAGATTTCACCTTTTAATTTTATTGCAATTAGTGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACGAGGCACATTTTTTTGACAcc                                                                                 >  2:402538/1‑140 (MQ=255)
                                               ttCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACAcc                                                                                 >  1:730864/1‑140 (MQ=255)
                                                tCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCt                                                                                <  1:668745/140‑1 (MQ=255)
                                                 cATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCtt                                                                               >  1:487237/1‑140 (MQ=255)
                                                 cATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCtt                                                                               >  1:919908/1‑140 (MQ=255)
                                                   tAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTtca                                                                             >  1:761112/1‑140 (MQ=255)
                                                      ccTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTtcatca                                                                          <  2:215268/140‑1 (MQ=255)
                                                       cTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCaa                                                                         >  1:901625/1‑140 (MQ=255)
                                                       cTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCCTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCaa                                                                         <  1:441601/140‑1 (MQ=255)
                                                         gcgcCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCaa                                                                         <  2:535220/138‑1 (MQ=255)
                                                         gcgcCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCaa                                                                         >  1:535220/1‑138 (MQ=255)
                                                         gcgcCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAgt                                                                       >  1:163828/1‑140 (MQ=255)
                                                         gcgcCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAgt                                                                       >  1:581156/1‑140 (MQ=255)
                                                         gcgcCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAgt                                                                       >  2:632674/1‑140 (MQ=255)
                                                                  gCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACg                                                              <  2:773900/140‑1 (MQ=255)
                                                                    aGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACg                                                              <  2:355076/138‑1 (MQ=255)
                                                                    aGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACg                                                              >  1:355076/1‑138 (MQ=255)
                                                                       cTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGtt                                                            >  2:117270/1‑137 (MQ=255)
                                                                       cTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGtt                                                            <  1:117270/137‑1 (MQ=255)
                                                                          tttctttcAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGa                                                      <  2:1001433/140‑1 (MQ=255)
                                                                              tttcAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGa                                                  <  2:761112/140‑1 (MQ=255)
                                                                                tcAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGAcc                                                >  1:407744/1‑140 (MQ=255)
                                                                                  aGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCAt                                              <  2:61010/140‑1 (MQ=255)
                                                                                    aTTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCg                                            <  2:678267/140‑1 (MQ=255)
                                                                                       tCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGata                                         >  1:603186/1‑140 (MQ=255)
                                                                                        cACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGCTTTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGata                                         >  2:481943/1‑140 (MQ=255)
                                                                                         aCCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATc                                       <  1:222801/140‑1 (MQ=255)
                                                                                           cTTTTCATTTCATTGCAATTAGAGTTCCCAGAAATTCGGC‑ATTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCaa                                     <  2:901625/140‑1 (MQ=255)
                                                                                           cTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCaa                                     <  1:632674/140‑1 (MQ=255)
                                                                                           cTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCaa                                     <  1:291861/140‑1 (MQ=255)
                                                                                              ttAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACca                                  <  2:407744/140‑1 (MQ=255)
                                                                                              ttAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACca                                  <  1:660204/140‑1 (MQ=255)
                                                                                                aaTTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACcaca                                <  1:827821/140‑1 (MQ=255)
                                                                                                aaTTTCATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACcaca                                <  2:301093/140‑1 (MQ=255)
                                                                                                     cATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACCACAGTGaa                           >  2:259187/1‑140 (MQ=255)
                                                                                                     cATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACCACAGTGaa                           <  2:487237/140‑1 (MQ=255)
                                                                                                     cATTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACCACAGTGaa                           <  2:163828/140‑1 (MQ=255)
                                                                                                      aTTGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACCACAGTGAAt                          <  2:730864/140‑1 (MQ=255)
                                                                                                        tGCAATTAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACCACAGTGAATgg                        >  1:41079/1‑140 (MQ=255)
                                                                                                             ttAGAGTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACCACAGTGAATGGGGttt                   >  2:184160/1‑140 (MQ=255)
                                                                                                               agagTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACCACAGTGAATGGGGTTTCt                 >  2:478314/1‑140 (MQ=255)
                                                                                                                 agTTGCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACCACAGTGAATGGGGTTTCttt               >  2:740168/1‑140 (MQ=255)
                                                                                                                     gCCAGAAATTCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACCACAGTGAATGGGGTTTCTTTAttt           >  2:355189/1‑140 (MQ=255)
                                                                                                                       cAGAAATTCGGCTTTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACCACAGTGAATGGGGTTTCTTTAtttt          <  1:481943/140‑1 (MQ=255)
                                                                                                                              tCGGC‑TTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACCACAGTGAATGGGGTTTCTTTATTTTCTGTTTTa  <  1:259187/140‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                       
ATTAAAATTCGTTTTGTTCAGTGAATGATCTTGCCGGATACACACTGTTCATAGCCTGCGCCATACGCAGGCTATTTCTTTCAGATTTCACCTTTTAATTTCATTGCAATTAGAGTTGCCAGAAATTCGGCTTTTTTTTCTGCGGGCAGATTCTTTCCGATATGCACCAGGCACATTTTTTTGACACCTTCATCAAGTGTTTTTACGTTGCCTGATGGACCATCGATATCAACCACAGTGAATGGGGTTTCTTTATTTTCTGTTTTA  >  NC_000913/1417408‑1417674

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A