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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,572,756 T→A 20.5% intergenic (+1524/‑255) yibH → / → ysaB hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,572,7560TA20.5% 249.5 / 60.8 117intergenic (+1524/‑255)yibH/ysaBhypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (41/52);  new base A (14/10);  total (55/62)
Fisher's exact test for biased strand distribution p-value = 2.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.86e-01

Only 100 of 122 total aligned reads displayed.

ATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGCAGTCTGATG  >  minE/2572687‑2572825
                                                                     |                                                                     
aTACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGt                                                                       >  1:2729850/1‑70 (MQ=255)
    tGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGtt                                                                      <  1:4968894/67‑1 (MQ=255)
      aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATg                                                                  >  1:943676/1‑69 (MQ=255)
      aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt                                                                <  1:1445588/71‑1 (MQ=255)
        aaaaaTTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTAc                                                              >  1:1167399/1‑71 (MQ=255)
         aaaaTTCCACCTACCTTCCAGCCCAATCGGAGCATGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTAcc                                                             >  1:4425874/1‑71 (MQ=255)
             ttCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGat                                                          >  1:3171790/1‑70 (MQ=255)
               ccACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGataa                                                        <  1:5065269/70‑1 (MQ=255)
                cACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGataat                                                       <  1:2640986/70‑1 (MQ=255)
                  cctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGt                                                    <  1:2116581/71‑1 (MQ=255)
                     acctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTta                                                  >  1:2439551/1‑70 (MQ=255)
                      cctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTTCGGTTAATGTTACCGATAATAGTta                                                  <  1:3063471/69‑1 (MQ=255)
                      cctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGa                                                           <  1:3796863/60‑1 (MQ=255)
                      cctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTta                                                  <  1:5310379/69‑1 (MQ=255)
                      cctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTta                                                  <  1:4763221/69‑1 (MQ=255)
                       ctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAg                                               <  1:5513053/71‑1 (MQ=255)
                         tCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAg                                               >  1:1695969/1‑69 (MQ=255)
                          ccAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTTCTGCGGTTAATGTTACCGATAATAGTTATAGt                                              <  1:5113808/69‑1 (MQ=255)
                          ccAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTa                                             <  1:5045414/70‑1 (MQ=255)
                           cAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTa                                             >  1:1811317/1‑69 (MQ=255)
                           cAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTa                                             >  1:4094487/1‑69 (MQ=255)
                           cAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTa                                             >  1:2144679/1‑69 (MQ=255)
                              ccccATCGGGTCCTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGcc                                        <  1:1764035/71‑1 (MQ=255)
                              ccccATCGGGTCCTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGcc                                        >  1:2273757/1‑71 (MQ=255)
                              cccAATCGGGTCCGGGGTGATATACCGCCCCTGCAACGGATCGTAGTGCCGGTGACGGTTATAGTACAGcc                                        >  1:64164/1‑71 (MQ=255)
                               cccaTCGGGTCCTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGccc                                       >  1:1898110/4‑71 (MQ=255)
                               ccAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGccc                                       >  1:2761371/1‑71 (MQ=255)
                                cAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGata                                                         >  1:3425088/1‑52 (MQ=255)
                                cAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCt                                      <  1:28268/71‑1 (MQ=255)
                                 caTCGGGTCCTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTg                                     <  1:2543541/70‑1 (MQ=255)
                                 caTCGGGTCCTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTg                                     <  1:3753246/70‑1 (MQ=255)
                                 aaTCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTaa                                                                    <  1:4299080/40‑1 (MQ=255)
                                  aTCGGGTCCTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGa                                    >  1:3363095/1‑71 (MQ=255)
                                  aTCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt                                                                >  1:2463427/1‑43 (MQ=255)
                                   tCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAt                                   >  1:4835131/1‑71 (MQ=255)
                                   tCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAt                                   >  1:2551937/1‑71 (MQ=255)
                                     ggAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGataata                                                      >  1:4172927/1‑50 (MQ=255)
                                     ggAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAtt                                  >  1:5074099/1‑70 (MQ=255)
                                     ggAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtc                                 <  1:3677966/71‑1 (MQ=255)
                                        tccTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATtcctc                              <  1:2827269/70‑1 (MQ=255)
                                        tccTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATtcctc                              <  1:5675327/70‑1 (MQ=255)
                                         ccTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGt                                              <  1:5209863/54‑1 (MQ=255)
                                         ccTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatca                             >  1:1458927/1‑71 (MQ=255)
                                          cTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat                            <  1:1215386/71‑1 (MQ=255)
                                           tGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGt                                              <  1:1550200/52‑1 (MQ=255)
                                           tGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTAc                                            >  1:3606836/1‑54 (MQ=255)
                                           tGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat                            >  1:4255053/1‑70 (MQ=255)
                                           tGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATtcctcat                            >  1:4848809/1‑70 (MQ=255)
                                            gggtgaTATACCGCCCCTGCAACGGATCGTAGTGCCGGTGACGGTTATAGTACAGCCCCGACtcctcatca                          <  1:3320751/69‑1 (MQ=255)
                                            gAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAg                                                     <  1:5317765/44‑1 (MQ=255)
                                             ggtgaTATACCGCCCCTGCAACGGATCGTAGTGCCGGTGACGGTTATAGTACAGCCCCGACTcctcatcat                         <  1:3500579/70‑1 (MQ=255)
                                             aGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAg                                                     <  1:375271/43‑1 (MQ=255)
                                             aGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                          <  1:4024081/70‑1 (MQ=255)
                                             aGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                          >  1:4364238/1‑70 (MQ=255)
                                             aGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTcatcatcat                         <  1:9140/71‑1 (MQ=255)
                                              gtgtTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAtt                                  >  1:4311450/1‑61 (MQ=255)
                                              gtgtTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAtt                                  >  1:1850727/1‑61 (MQ=255)
                                              gtgtTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAtt                                  >  1:3075723/1‑61 (MQ=255)
                                              gtgaTATACCGCCCCTGCAACGGATCGTAGTGCCGGTGACGGTTATAGTACAGCCCCGACtcctcat                            <  1:4888930/67‑1 (MQ=255)
                                               taatataCCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATtcctcat                            <  1:1756528/63‑1 (MQ=255)
                                                gtTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat                            <  1:3750460/65‑1 (MQ=255)
                                                gtTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat                            <  1:3995348/65‑1 (MQ=255)
                                                aatataCCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATTCCTCATCAtgct                      >  1:3625482/3‑71 (MQ=255)
                                                 ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCt                                      <  1:459614/54‑1 (MQ=255)
                                                 ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCt                                      <  1:4608315/54‑1 (MQ=255)
                                                 ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCt                                      <  1:5120786/54‑1 (MQ=255)
                                                 ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCAtact                      <  1:704595/70‑1 (MQ=255)
                                                 ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCAtact                      <  1:1963142/70‑1 (MQ=255)
                                                 atataCCGCCCCTGCAACGGATCGTAGTGCCGGTGACGGTTATAGTACAGcccc                                      >  1:1408611/2‑53 (MQ=255)
                                                 atataCCGCCCCTGCAACGGATCGTAGTGCCGGTGACGGTTATAGTACAGCCCCGACTCCTCATCAtgctg                     <  1:1260426/70‑2 (MQ=255)
                                                 atataCCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATtcctc                              >  1:2377207/2‑62 (MQ=255)
                                                   ataCCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTtata                                                >  1:1599657/1‑42 (MQ=255)
                                                   ataCCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTtata                                                >  1:3483156/1‑42 (MQ=255)
                                                   ataCCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTtat                                                 >  1:4843679/1‑41 (MQ=255)
                                                    taCCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGcc                                        >  1:3598182/1‑49 (MQ=255)
                                                    taCCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATTCCTCATCATGctgctg                  >  1:1084867/1‑71 (MQ=255)
                                                     aCCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat                            <  1:3216827/60‑1 (MQ=255)
                                                         ccccTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCg             >  1:1675088/1‑71 (MQ=255)
                                                           ccTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGa                                    >  1:4672802/1‑46 (MQ=255)
                                                           ccTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGa                                    >  1:707945/1‑46 (MQ=255)
                                                           ccTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCAtact                      <  1:4925133/60‑1 (MQ=255)
                                                           ccTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATactactact                <  1:2410494/66‑1 (MQ=255)
                                                           ccTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCgg            >  1:1158939/1‑70 (MQ=255)
                                                            ctgctgCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                          <  1:3793395/55‑1 (MQ=255)
                                                            ctgctgCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                          <  1:1131489/55‑1 (MQ=255)
                                                            ctgctgCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                          <  1:878015/55‑1 (MQ=255)
                                                            ctgctgCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                          <  1:2079703/55‑1 (MQ=255)
                                                            ctgctgCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGCa          <  1:3059692/71‑1 (MQ=255)
                                                             tgctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                          <  1:105533/54‑1 (MQ=255)
                                                             tgctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                          <  1:3481780/54‑1 (MQ=255)
                                                             tgctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                          <  1:4509804/54‑1 (MQ=255)
                                                             tgctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGCAg         >  1:3132992/1‑71 (MQ=255)
                                                              gctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat                            <  1:946158/51‑1 (MQ=255)
                                                              gctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat                            <  1:1960161/51‑1 (MQ=255)
                                                              gctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGc           >  1:3048195/1‑68 (MQ=255)
                                                               ctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGCAGTc       >  1:67307/1‑71 (MQ=255)
                                                                  cGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGCAGTCtg     <  1:4764864/70‑1 (MQ=255)
                                                                     ttAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGCAGTCtgat   <  1:5478436/69‑1 (MQ=255)
                                                                     ttAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGCAGTCtgat   <  1:2148182/69‑1 (MQ=255)
                                                                     ttAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGCAGTCtgat   <  1:3604419/69‑1 (MQ=255)
                                                                     |                                                                     
ATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGCAGTCTGATG  >  minE/2572687‑2572825

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A