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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,476,857 G→A 29.1% S56S (TCC→TCT)  inaA ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,476,8570GA29.1% 174.9 / 74.3 164S56S (TCC→TCT) inaAconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (48/68);  new base A (24/24);  total (72/92)
Fisher's exact test for biased strand distribution p-value = 3.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.62e-01

Only 100 of 166 total aligned reads displayed.

CCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCTTTTTGCCGTTGCGCTCGACGCATTGCA  >  minE/1476790‑1476924
                                                                   |                                                                   
cccGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACgg                                                                    <  1:383781/69‑1 (MQ=255)
 ccGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGa                                                                   <  1:2454208/69‑1 (MQ=255)
     tCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               <  1:1893331/69‑1 (MQ=255)
     tCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               <  1:722479/69‑1 (MQ=255)
     tCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               <  1:2615875/69‑1 (MQ=255)
     tCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               <  1:3071948/69‑1 (MQ=255)
     tCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               <  1:422885/69‑1 (MQ=255)
     tCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               <  1:2701116/69‑1 (MQ=255)
     tCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               <  1:2826800/69‑1 (MQ=255)
     tCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               <  1:1449878/69‑1 (MQ=255)
      ccggTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               >  1:1465193/4‑68 (MQ=255)
      ccAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               >  1:3361548/1‑68 (MQ=255)
      ccAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               >  1:3318917/1‑68 (MQ=255)
      ccAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               >  1:2099692/1‑68 (MQ=255)
      ccAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               >  1:2671850/1‑68 (MQ=255)
      ccAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               >  1:2393019/1‑68 (MQ=255)
      ccAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               >  1:1014871/1‑68 (MQ=255)
      ccAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               >  1:2418077/1‑68 (MQ=255)
      ccAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               >  1:2545247/1‑68 (MQ=255)
      ccAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               >  1:551902/1‑68 (MQ=255)
      ccAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               >  1:88029/1‑68 (MQ=255)
      ccAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGa                                                               >  1:1144766/1‑68 (MQ=255)
      ccAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTAAGGAAtta                                                               >  1:33980/1‑66 (MQ=255)
      ccAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGCCCGAACGGATAACGTACGGa                                                                   >  1:1956183/1‑64 (MQ=255)
         gTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAAt                                                                 <  1:632142/63‑1 (MQ=255)
         gTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAAt                                                                 <  1:2275822/63‑1 (MQ=255)
         gTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAAt                                                                 <  1:609291/63‑1 (MQ=255)
         gTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAAt                                                                 <  1:2874918/63‑1 (MQ=255)
         gTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAAt                                                                 <  1:211396/63‑1 (MQ=255)
         gTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAAt                                                                 <  1:1595978/63‑1 (MQ=255)
         gTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAAt                                                                 <  1:2395734/63‑1 (MQ=255)
         gTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAAt                                                                 <  1:407740/63‑1 (MQ=255)
         gTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAAt                                                                 <  1:3272496/63‑1 (MQ=255)
         gTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAAt                                                                 <  1:333238/63‑1 (MQ=255)
         gTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAAt                                                                 <  1:3382582/63‑1 (MQ=255)
            cTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAgat                                                        <  1:91439/69‑1 (MQ=255)
            cTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAgat                                                        <  1:815436/69‑1 (MQ=255)
            cTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAgat                                                        <  1:237834/69‑1 (MQ=255)
            cTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAgat                                                        <  1:2508617/69‑1 (MQ=255)
            cTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAgat                                                        <  1:1201741/69‑1 (MQ=255)
            cTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAgat                                                        <  1:3058064/69‑1 (MQ=255)
            cTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAgat                                                        <  1:1844751/69‑1 (MQ=255)
            cTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAg                                                          >  1:2002178/1‑67 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAATGAAACAg                                                          >  1:2753627/1‑62 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAATGAAACAg                                                          >  1:488046/1‑62 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAATGAAACAg                                                          >  1:2899739/1‑62 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAATGAAACAg                                                          >  1:2925852/1‑62 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAATGAAACAg                                                          >  1:2558846/1‑62 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAATGAAACAg                                                          >  1:360816/1‑62 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAATGAAACAg                                                          >  1:2415880/1‑62 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAATGAAACAg                                                          >  1:1923958/1‑62 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAATGAAACAg                                                          >  1:1288660/1‑62 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAATGAAACAg                                                          >  1:1181977/1‑62 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAATGAAACAg                                                          >  1:2348270/1‑62 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAATGAAACAg                                                          >  1:1067713/1‑62 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGGTAACGTACAGAATGAAACAg                                                          >  1:2408989/1‑62 (MQ=255)
                 aTTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGatgatg                                                    <  1:1348798/68‑1 (MQ=255)
                   tACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGt                                                 <  1:2800688/69‑1 (MQ=255)
                   tACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGt                                                 <  1:1643023/69‑1 (MQ=255)
                   tACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGt                                                 <  1:2052899/69‑1 (MQ=255)
                   tACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGt                                                 <  1:1869818/69‑1 (MQ=255)
                   tACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGt                                                 <  1:2025590/69‑1 (MQ=255)
                   tACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGt                                                 <  1:1959069/69‑1 (MQ=255)
                   tACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGt                                                 <  1:3126239/69‑1 (MQ=255)
                    aCCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGaa                                                              <  1:855674/55‑1 (MQ=255)
                    aCCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGaa                                                              <  1:534412/55‑1 (MQ=255)
                    aCCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGaa                                                              <  1:497831/55‑1 (MQ=255)
                    aCCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGaa                                                              <  1:1919081/55‑1 (MQ=255)
                    aCCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGaa                                                              <  1:1016622/55‑1 (MQ=255)
                    aCCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGt                                                 <  1:2233755/68‑1 (MQ=255)
                       gCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATg                                             <  1:1903601/69‑1 (MQ=255)
                       gCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATg                                             <  1:2138206/69‑1 (MQ=255)
                       gCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATg                                             <  1:1612426/69‑1 (MQ=255)
                          aCCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATgcgc                                          >  1:1118002/1‑69 (MQ=255)
                                        cGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCtt                            >  1:3116099/1‑69 (MQ=255)
                                        cGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCtt                            <  1:1840143/69‑1 (MQ=255)
                                        cGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCtt                            >  1:635297/1‑69 (MQ=255)
                                         gTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTtaca                                    <  1:3233330/60‑1 (MQ=255)
                                         gTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTtaca                                    <  1:2642753/60‑1 (MQ=255)
                                         gTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTtaca                                    <  1:3353384/60‑1 (MQ=255)
                                         gTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTtaca                                    <  1:2309578/60‑1 (MQ=255)
                                         gTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTtaca                                    <  1:1724869/60‑1 (MQ=255)
                                         gTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTtaca                                    <  1:1652050/60‑1 (MQ=255)
                                         gTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCttt                           >  1:566520/1‑69 (MQ=255)
                                         gTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCttt                           >  1:394331/1‑69 (MQ=255)
                                         gTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCttt                           >  1:1717513/1‑69 (MQ=255)
                                         gTTGGTCGGCCGAACGGATAACGTACGGAACGAAACAGATGATGCGTCATGCGCTTtaca                                    <  1:1084408/60‑1 (MQ=255)
                                                       cGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTtaca                                    <  1:3219413/46‑1 (MQ=255)
                                                       cGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTtaca                                    <  1:2711979/46‑1 (MQ=255)
                                                       cGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTtaca                                    <  1:2259193/46‑1 (MQ=255)
                                                       cGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTtaca                                    <  1:2800662/46‑1 (MQ=255)
                                                       cGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTtaca                                    <  1:2034597/46‑1 (MQ=255)
                                                        ggATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTtaca                                    <  1:264433/45‑1 (MQ=255)
                                                                tACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCTTTTTGCCGTTGCGCTCGACGCATTg    >  1:519285/1‑69 (MQ=255)
                                                                tACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCTTTTTGCCGTTGCGCTCGACGCATTg    >  1:517725/1‑69 (MQ=255)
                                                                tACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCTTTTTGCCGTTGCGCTCGACGCATTg    >  1:793433/1‑69 (MQ=255)
                                                                tACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCTTTTTGCCGTTGCGCTCGACGCATTg    >  1:822083/1‑69 (MQ=255)
                                                                tACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCTTTTTGCCGTTGCGCTCGACGCATTg    >  1:3284216/1‑69 (MQ=255)
                                                                tACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCTTTTTGCCGTTGCGCTCGACGCATTg    >  1:1061441/1‑69 (MQ=255)
                                                                tACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCTTTTTGCCGTTGCGCTCGACGCATTg    >  1:2523243/1‑69 (MQ=255)
                                                                   |                                                                   
CCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCCGAACGGATAACGTACGGAATGAAACAGATGATGCGTCATGCGCTTTACATACAGCTTTTTGCCGTTGCGCTCGACGCATTGCA  >  minE/1476790‑1476924

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A