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 2,572,752 G→A 21.5% intergenic (+1520/‑259) yibH → / → ysaB hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,572,7520GA21.5% 214.8 / 52.9 112intergenic (+1520/‑259)yibH/ysaBhypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (48/39);  new base A (14/10);  total (62/50)
Fisher's exact test for biased strand distribution p-value = 8.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.83e-01

Only 100 of 136 total aligned reads displayed.

AACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGCAGTC  >  minE/2572682‑2572820
                                                                      |                                                                    
  cGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGATATATCGCCCCTGCAGCg                                                                    <  1:4503678/71‑1 (MQ=255)
  cGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCCTGCAGCg                                                                    <  1:3995756/71‑1 (MQ=255)
  cGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCg                                                                    >  1:5666993/1‑71 (MQ=255)
   ggATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCCTGCAGCgg                                                                   >  1:5171066/1‑71 (MQ=255)
     aTACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGt                                                                  >  1:2729850/1‑70 (MQ=255)
      tACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGATATATCGCCCCTGCAGCgggtc                                                                <  1:2850444/71‑4 (MQ=255)
         tGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGtt                                                                 <  1:4968894/67‑1 (MQ=255)
          gATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCAGCAGCgg                                                                   >  1:4979797/1‑64 (MQ=255)
          gATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCAGCAGCgg                                                                   >  1:1934447/1‑64 (MQ=255)
           aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATg                                                             >  1:943676/1‑69 (MQ=255)
           aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt                                                           <  1:1445588/71‑1 (MQ=255)
            tAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCagcagc                                                                     <  1:1807372/60‑1 (MQ=255)
            tAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCtgctgc                                                                     <  1:2339800/60‑1 (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)
                      acctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCtgctgc                                                                     <  1:514564/50‑1 (MQ=255)
                      acctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCtgctgc                                                                     <  1:309814/50‑1 (MQ=255)
                       cctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGt                                               <  1:2116581/71‑1 (MQ=255)
                        ctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCtgctgc                                                                     <  1:399991/48‑1 (MQ=255)
                        ctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCg                                                                    >  1:2150441/1‑49 (MQ=255)
                        ctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGt                                               >  1:2631853/1‑70 (MQ=255)
                          acctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTta                                             >  1:2439551/1‑70 (MQ=255)
                           cctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTTCGGTTAATGTTACCGATAATAGTta                                             <  1:3063471/69‑1 (MQ=255)
                           cctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGa                                                      <  1:3796863/60‑1 (MQ=255)
                           cctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTta                                             <  1:4763221/69‑1 (MQ=255)
                           cctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTta                                             <  1:5310379/69‑1 (MQ=255)
                            ctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAg                                          >  1:1943673/1‑71 (MQ=255)
                            ctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAg                                          <  1:5513053/71‑1 (MQ=255)
                             ttCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTa                                                          >  1:815782/1‑54 (MQ=255)
                               ccAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTTCTGCGGTTAATGTTACCGATAATAGTTATAGt                                         <  1:5113808/69‑1 (MQ=255)
                               ccAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTa                                        <  1:5045414/70‑1 (MQ=255)
                                cAGCCCAATCGGATCCTGAGTGATATACCGCCCCTGCAGCgg                                                                   >  1:701797/1‑42 (MQ=255)
                                cAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTa                                        >  1:4094487/1‑69 (MQ=255)
                                cAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTa                                        >  1:2144679/1‑69 (MQ=255)
                                cAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTa                                        >  1:1811317/1‑69 (MQ=255)
                                cAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTAc                                       <  1:2124118/70‑1 (MQ=255)
                                   cccAATCGGGTCCGGGGTGATATACCGCCCCTGCAACGGATCGTAGTGCCGGTGACGGTTATAGTACAGcc                                   >  1:64164/1‑71 (MQ=255)
                                    cccaTCGGGTCCTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGccc                                  >  1:1181916/4‑71 (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)
                                       aTCGGGTCCTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCACTGa                               >  1:3547067/1‑71 (MQ=255)
                                       aTCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt                                                           >  1:2463427/1‑43 (MQ=255)
                                        tCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAt                              >  1:4835131/1‑71 (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)
                                              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)
                                                  ggtgaTATACCGCCCCTGCAACGGATCGTAGTGCCGGTGACGGTTATAGTACAGCCCCGACTcctcatcat                    <  1:3500579/70‑1 (MQ=255)
                                                   gtgtTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAtt                             >  1:3075723/1‑61 (MQ=255)
                                                   gtgtTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAtt                             >  1:4311450/1‑61 (MQ=255)
                                                   gtgtTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAtt                             >  1:1850727/1‑61 (MQ=255)
                                                   gtgaTATACCGCCCCTGCAACGGATCGTAGTGCCGGTGACGGTTATAGTACAGCCCCGACtcctcat                       <  1:4888930/67‑1 (MQ=255)
                                                    taatataCCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATtcctcat                       <  1:1756528/63‑1 (MQ=255)
                                                     gtTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat                       <  1:3995348/65‑1 (MQ=255)
                                                     gtTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat                       <  1:3750460/65‑1 (MQ=255)
                                                      ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCt                                 <  1:459614/54‑1 (MQ=255)
                                                      ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCt                                 <  1:4608315/54‑1 (MQ=255)
                                                      ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTcatcatcat                    <  1:1729571/67‑1 (MQ=255)
                                                      atataCCGCCCCTGCAACGGATCGTAGTGCCGGTGACGGTTATAGTACAGcccc                                 >  1:1408611/2‑53 (MQ=255)
                                                      atataCCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATtcctc                         >  1:2377207/2‑62 (MQ=255)
                                                      atataCCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATTCCTCATCAtgctg                >  1:5647503/2‑70 (MQ=255)
                                                        ataCCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTtata                                           >  1:3483156/1‑42 (MQ=255)
                                                        ataCCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTtata                                           >  1:1599657/1‑42 (MQ=255)
                                                         taCCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGcc                                   >  1:3598182/1‑49 (MQ=255)
                                                         taCCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGcc                                   >  1:3381715/1‑49 (MQ=255)
                                                         taCCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATTCCTCATCATGctgctg             >  1:1084867/1‑71 (MQ=255)
                                                          aCCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat                       <  1:3216827/60‑1 (MQ=255)
                                                           ccGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTActgct           <  1:3679169/71‑1 (MQ=255)
                                                              ccccTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCg        >  1:1675088/1‑71 (MQ=255)
                                                                ccTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGa                               >  1:4672802/1‑46 (MQ=255)
                                                                ccTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGa                               >  1:707945/1‑46 (MQ=255)
                                                                ccTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGa                               >  1:4879658/1‑46 (MQ=255)
                                                                ccTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATactactact           <  1:2410494/66‑1 (MQ=255)
                                                                ccTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGc      <  1:527883/71‑1 (MQ=255)
                                                                 ctgctgCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                     <  1:2079703/55‑1 (MQ=255)
                                                                 ctgctgCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                     <  1:3793395/55‑1 (MQ=255)
                                                                 ctgctgCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                     <  1:1131489/55‑1 (MQ=255)
                                                                 ctgctgCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                     <  1:878015/55‑1 (MQ=255)
                                                                  tgctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                     <  1:303116/54‑1 (MQ=255)
                                                                  tgctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                     <  1:4503456/54‑1 (MQ=255)
                                                                  tgctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca                     <  1:105533/54‑1 (MQ=255)
                                                                  tgctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGCAg    >  1:3132992/1‑71 (MQ=255)
                                                                   gctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat                       <  1:1960161/51‑1 (MQ=255)
                                                                   gctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat                       <  1:946158/51‑1 (MQ=255)
                                                                   gctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGc      >  1:3048195/1‑68 (MQ=255)
                                                                    ctgcGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGCAGTc  >  1:67307/1‑71 (MQ=255)
                                                                      |                                                                    
AACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTACTGCTGCGGCAGTC  >  minE/2572682‑2572820

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