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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,041,438 G→A 46.5% D32N (GAT→AAT)  yqiI → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,041,4380GA46.5% 18.5 / 112.4 86D32N (GAT→AAT) yqiIconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (25/21);  new base A (22/18);  total (47/39)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

TTTTTTTATGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAGGTGATAAAATCT  >  minE/2041371‑2041507
                                                                   |                                                                     
tttttttATGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATa                                                                    >  1:1152225/1‑71 (MQ=255)
 ttttttATGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGgag                                                                       >  1:2628754/1‑67 (MQ=255)
  tttttATGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATAcc                                                                  >  1:3856355/1‑71 (MQ=255)
  tttttATGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATAcc                                                                  >  1:3634438/1‑71 (MQ=255)
    tttATGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGt                                                                >  1:1280694/1‑71 (MQ=255)
      tATGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGtt                                                               <  1:562597/70‑1 (MQ=255)
       aTGGGTTTTAGTTCATTAGCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTg                                                              <  1:871471/70‑1 (MQ=255)
        tGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATAACGTTGt                                                             >  1:1600578/1‑70 (MQ=255)
        tGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGt                                                             >  1:2265995/1‑70 (MQ=255)
        tGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGt                                                             >  1:2261417/1‑70 (MQ=255)
         gggTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCa                                                           >  1:527098/1‑71 (MQ=255)
          ggTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCa                                                           <  1:3033181/70‑1 (MQ=255)
          ggTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCAt                                                          <  1:605852/71‑1 (MQ=255)
          ggTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCAt                                                          <  1:3412174/71‑1 (MQ=255)
           gTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCAtt                                                         <  1:289488/71‑1 (MQ=255)
           gTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCAtt                                                         >  1:1419466/1‑71 (MQ=255)
            ttttAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTg                                                        >  1:1836003/1‑71 (MQ=255)
             tttAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTgg                                                       >  1:132476/1‑71 (MQ=255)
              ttAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGt                                                      >  1:1437825/1‑71 (MQ=255)
              ttAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGt                                                      >  1:608665/1‑71 (MQ=255)
              ttAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGt                                                      >  1:3925757/1‑71 (MQ=255)
              ttAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGt                                                      >  1:1525930/1‑71 (MQ=255)
               tAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGt                                                      <  1:2127047/70‑1 (MQ=255)
               tAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGt                                                      <  1:3502539/70‑1 (MQ=255)
                aGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGtt                                                     <  1:492131/70‑1 (MQ=255)
                aGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGtt                                                     <  1:2030411/70‑1 (MQ=255)
                     aTTACCTGCATGGGCAATGGACTGCTATGCTGAACTTGAAGGTGGAGATACCGTTGTCATTGGTTACGTa                                                <  1:3772311/70‑1 (MQ=255)
                     aTTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGt                                                      <  1:2131327/64‑1 (MQ=255)
                      ttACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTAc                                               >  1:2842848/1‑70 (MQ=255)
                      ttACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTAc                                               >  1:2532754/1‑70 (MQ=255)
                       tACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTAcc                                              >  1:2792558/1‑70 (MQ=255)
                        aCCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCa                                                           >  1:3005392/1‑56 (MQ=255)
                        aCCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTAcc                                              >  1:686378/1‑69 (MQ=255)
                        aCCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTAcc                                              >  1:134886/1‑69 (MQ=255)
                         ccTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAg                                           <  1:46732/71‑1 (MQ=255)
                         ccTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTgg                                                       <  1:861549/59‑1 (MQ=255)
                          cTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATa                                                                    >  1:1014787/1‑45 (MQ=255)
                            gCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTAcc                                              <  1:1697998/65‑1 (MQ=255)
                             cATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGt                                                                <  1:3140066/46‑1 (MQ=255)
                              aTGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAAtct                                      <  1:943643/71‑1 (MQ=255)
                               tGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATAcc                                                                  <  1:3721910/42‑1 (MQ=255)
                                 ggCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATctct                                    <  1:3449138/70‑1 (MQ=255)
                                 ggCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATctct                                    <  1:603309/70‑1 (MQ=255)
                                 ggCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTa                                   <  1:3283070/71‑1 (MQ=255)
                                  gCAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTAt                                  >  1:3909506/1‑71 (MQ=255)
                                   cAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTg                                                              <  1:3209902/42‑1 (MQ=255)
                                   cAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTgg                                                       <  1:2408612/49‑1 (MQ=255)
                                   cAATGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATc                                 <  1:2703489/71‑1 (MQ=255)
                                    aaTGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCTAGAATCTCTATcc                                >  1:3509715/1‑71 (MQ=255)
                                     aTGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCaa                                            >  1:104708/1‑58 (MQ=255)
                                     aTGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATccc                               <  1:3195374/71‑1 (MQ=255)
                                     aTGGACTGCTATGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATccc                               >  1:1138596/1‑71 (MQ=255)
                                        gACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGt                                                      >  1:2102183/1‑45 (MQ=255)
                                        gACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGt                                                      >  1:3870836/1‑45 (MQ=255)
                                        gACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGt                                                      >  1:3632393/1‑45 (MQ=255)
                                           tGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGa                         >  1:1782755/1‑71 (MQ=255)
                                            gCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGtt                                                     >  1:2216529/1‑42 (MQ=255)
                                             cTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGa                         <  1:3829628/69‑1 (MQ=255)
                                               aTGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATgg                      >  1:3085961/1‑70 (MQ=255)
                                               aTGCTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATgg                      >  1:2270215/1‑70 (MQ=255)
                                                tGCTGAACATGAAGGTGGAGATTCCGTTGTCATTGGTTACGTACCAAGa                                          <  1:1636178/49‑1 (MQ=255)
                                                 gCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATg                       >  1:526369/1‑67 (MQ=255)
                                                  cTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTaa                   <  1:1889787/70‑1 (MQ=255)
                                                  cTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTaa                   >  1:1492351/1‑70 (MQ=255)
                                                  cTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTaaa                  <  1:2057175/71‑1 (MQ=255)
                                                  cTGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTaa                   >  1:917171/1‑70 (MQ=255)
                                                   tGAACATGAAGGTGGAAATACCGTTGTCATTGGTTACCTACCaa                                            <  1:506919/44‑1 (MQ=38)
                                                    gAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAAtctc                                     <  1:2604695/50‑1 (MQ=255)
                                                    gAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAAtctc                                     <  1:3951285/50‑1 (MQ=255)
                                                    gAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCa                             <  1:41711/58‑1 (MQ=255)
                                                    gAACATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGa                         <  1:1154296/62‑1 (MQ=255)
                                                     aaCATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTaaaaa                <  1:1487657/70‑1 (MQ=255)
                                                     aaCATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTaaaaa                <  1:2967618/70‑1 (MQ=255)
                                                     aaCATCAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAAtct                                      <  1:86977/48‑1 (MQ=38)
                                                      aCATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGa                                          >  1:3229302/1‑43 (MQ=255)
                                                      aCATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGAt                        >  1:3854631/1‑61 (MQ=255)
                                                       cATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAgg             >  1:1129933/1‑71 (MQ=255)
                                                       cATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAgg             >  1:1132380/1‑71 (MQ=255)
                                                       cATGAAGGTGGAAATACCGTTGTCATTGGTTACGTa                                                <  1:2317758/36‑1 (MQ=255)
                                                       cATGAAGGTGGAAATACCGTTGTCATTGGTTACGTACCAAGAAtc                                       >  1:2483257/1‑45 (MQ=255)
                                                          gAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAGGTGa          >  1:1555784/1‑71 (MQ=255)
                                                            aGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAgg             >  1:3574113/1‑66 (MQ=255)
                                                            aGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAGGTGAt         >  1:1507217/1‑70 (MQ=255)
                                                              gTGGAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCCATGGTAAAAAAGGTGATaaa      <  1:1296466/71‑1 (MQ=255)
                                                               tctagaTACCGTTGTCATTGGTTACGTAACAAGAATCTCTATCCCCAGAGATGGTAAAAAAGGTGATaaa      <  1:2572316/67‑1 (MQ=255)
                                                                ggAAATACCGTTGTCATTGGTTACGTACCAAGAAtc                                       >  1:3409459/1‑36 (MQ=255)
                                                                ggAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATg                       >  1:118906/1‑52 (MQ=255)
                                                                ggAAATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAGGTGATAAAAt    >  1:1239760/1‑71 (MQ=255)
                                                                  agaTACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGa                         <  1:2675063/48‑1 (MQ=255)
                                                                  agaTACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAGGTGATAAAATCt  <  1:443582/71‑1 (MQ=255)
                                                                   |                                                                     
TTTTTTTATGGGTTTTAGTTCATTACCTGCATGGGCAATGGACTGCTATGCTGAACATGAAGGTGGAGATACCGTTGTCATTGGTTACGTACCAAGAATCTCTATCCCCAGCGATGGTAAAAAAGGTGATAAAATCT  >  minE/2041371‑2041507

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