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 F28 I1 R1 163 52.9 1786516 99.3% 1774010 139.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,774,081 T→C V255A (GTC→GCC)  yfjW → CP4‑57 prophage; uncharacterized protein YfjW

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,774,0810TC96.7% 200.3 / ‑2.0 60V255A (GTC→GCC) yfjWCP4‑57 prophage; uncharacterized protein YfjW
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base C (34/24);  total (35/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

ATAATGAGGAATCATTTGGGTTTTTAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGTCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGTTCATACAAGGTGAATCCGC  >  NC_000913/2773952‑2774213
                                                                                                                                 |                                                                                                                                    
aTAATGAGGAATCATTTGGGTTTTTAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGgttgt                                                                                                                            <  1:611915/140‑1 (MQ=255)
 tAATGAGGAATCATTTGGGTTTTTAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGTCTCCgg                                                                                                                                >  2:822905/1‑135 (MQ=255)
 tAATGAGGAATCATTTGGGTTTTTAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGTCTCCgg                                                                                                                                <  1:822905/135‑1 (MQ=255)
  aaTGAGGAATCATTTGGGTTTTTAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTa                                                                                                                          >  2:773523/1‑140 (MQ=255)
  aaTGAGGAATCATTTGGGTTTTTAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTa                                                                                                                          <  1:33495/140‑1 (MQ=255)
    tGAGGAATCATTTGGGTTTTTAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATg                                                                                                                        <  2:576209/140‑1 (MQ=255)
    tGAGGAATCATTTGGGTTTTTAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATg                                                                                                                        >  2:275525/1‑140 (MQ=255)
          aTCATTTGGGTTTTTAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTc                                                                                                                  >  2:868089/1‑140 (MQ=255)
              tttGGGTTTTTAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGa                                                                                                              >  1:834407/1‑140 (MQ=255)
               ttGGGTTTTTAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGAt                                                                                                             <  1:786633/140‑1 (MQ=255)
                    tttttAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACt                                                                                                        <  2:306329/140‑1 (MQ=255)
                    tttttAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACt                                                                                                        <  1:22319/140‑1 (MQ=255)
                          aaTGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCaa                                                                                                  <  1:486715/140‑1 (MQ=255)
                                   aaaaCAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCt                                                                                         <  2:8823/140‑1 (MQ=255)
                                   aaaaCAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCt                                                                                         <  1:832870/140‑1 (MQ=255)
                                          acacacCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATg                                                                                    >  2:835036/1‑138 (MQ=255)
                                          acacacCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATg                                                                                    <  1:835036/138‑1 (MQ=255)
                                                      aTCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCtttt                                                                      <  1:275525/140‑1 (MQ=255)
                                                        cTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCt                                                                    <  1:565463/140‑1 (MQ=255)
                                                        cTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCt                                                                    >  2:656513/1‑140 (MQ=255)
                                                        cTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCt                                                                    >  2:358989/1‑140 (MQ=255)
                                                              gTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGt                                                              >  1:319514/1‑140 (MQ=255)
                                                                aaTCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTaa                                                            >  1:221447/1‑140 (MQ=255)
                                                                 aTCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTaaa                                                           >  1:599136/1‑140 (MQ=255)
                                                                       aaTGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCt                                                     <  1:358989/140‑1 (MQ=255)
                                                                         tGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAg                                                   >  2:414829/1‑140 (MQ=255)
                                                                            tAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAACGTAAAAAAGCTAGaaa                                                <  1:773523/140‑1 (MQ=255)
                                                                                 tGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATcaca                                           <  2:319514/140‑1 (MQ=255)
                                                                                     atataATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGa                                       <  2:834407/140‑1 (MQ=255)
                                                                                        taATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAAc                                    >  2:550891/1‑140 (MQ=255)
                                                                                         aaTGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACt                                   >  1:188364/1‑140 (MQ=255)
                                                                                         aaTGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACt                                   >  1:851888/1‑140 (MQ=255)
                                                                                           tGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTc                                 >  1:381728/1‑140 (MQ=255)
                                                                                             aTACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCa                               >  1:183931/1‑140 (MQ=255)
                                                                                             aTACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCa                               <  1:446024/140‑1 (MQ=255)
                                                                                              tACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCaa                              >  1:516003/1‑140 (MQ=255)
                                                                                              tACACAGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCaa                              >  2:12867/1‑140 (MQ=255)
                                                                                                cacaGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAatg                            >  2:607435/1‑140 (MQ=255)
                                                                                                cacaGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAatg                            >  2:541383/1‑140 (MQ=255)
                                                                                                cacaGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAatg                            >  1:319737/1‑140 (MQ=255)
                                                                                                cacaGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAata                            >  2:465443/1‑139 (MQ=255)
                                                                                                   aGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAatgatg                         >  1:621996/1‑140 (MQ=255)
                                                                                                   aGGGTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAatgatg                         >  1:149720/1‑140 (MQ=255)
                                                                                                     ggTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATggg                       >  1:600881/1‑140 (MQ=255)
                                                                                                     ggTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATggg                       >  2:278045/1‑140 (MQ=255)
                                                                                                     ggTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATggg                       >  1:723301/1‑140 (MQ=255)
                                                                                                      gTTTAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATgggg                      <  2:149720/140‑1 (MQ=255)
                                                                                                       tttAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACTGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGt                     <  2:621996/140‑1 (MQ=255)
                                                                                                       tttAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGt                     <  1:12867/140‑1 (MQ=255)
                                                                                                       tttAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGt                     >  1:392419/1‑140 (MQ=255)
                                                                                                       tttAAGTGGTGCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGt                     <  2:723301/140‑1 (MQ=255)
                                                                                                               gtgCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGTTCATACaa             >  1:792999/1‑140 (MQ=255)
                                                                                                               gtgCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGTTCATACaa             >  2:725202/1‑140 (MQ=255)
                                                                                                               gtgCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGTTCATACaa             >  1:56712/1‑140 (MQ=255)
                                                                                                                tgCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGTTCATACAAg            >  1:625198/1‑140 (MQ=255)
                                                                                                                 gCTGATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGTTCATACAAgg           >  1:883853/1‑140 (MQ=255)
                                                                                                                    gATATTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGTTCATACAAGGTGa        <  1:184453/140‑1 (MQ=255)
                                                                                                                       atTTATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGTTCATACAAGGTGAATc     <  2:625198/140‑1 (MQ=255)
                                                                                                                         ttATATTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGTTCATACAAGGTGAATCCg   <  2:353107/140‑1 (MQ=255)
                                                                                                                          tataTTGCCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGTTCATACAAGGTGAATCCGc  >  1:857274/1‑140 (MQ=255)
                                                                                                                                 |                                                                                                                                    
ATAATGAGGAATCATTTGGGTTTTTAAATGATAAAAAAACAGACACACCAACGTATCTGGATGTAATCAAAAATGGTAGTTTGATATATAATGATACACAGGGTTTAAGTGGTGCTGATATTTATATTGTCTCCGGTTGTTATGCCCTTCCAGATTTACTTCGCAATGTACCGCTTGATGCTAAAAAATCTTTTCTGAATGTAAAAAAGCTAGAAATCACACAGAAACTTCCAATGATGGGGTTCATACAAGGTGAATCCGC  >  NC_000913/2773952‑2774213

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A