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 2,642,710 C→A 42.8% S114S (TCC→TCA)  gntR → DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,642,7100CA42.8% 52.1 / 90.9 100S114S (TCC→TCA) gntRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (42/15);  new base A (19/23);  total (61/39)
Fisher's exact test for biased strand distribution p-value = 6.28e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.97e-01

ATCAGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACAC  >  minE/2642649‑2642760
                                                             |                                                  
aTCAAACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:2165931/69‑1 (MQ=255)
aTCAAACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:962021/69‑1 (MQ=255)
aTCAAACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:405906/69‑1 (MQ=255)
aTCAAACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:344418/69‑1 (MQ=255)
aTCAAACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:2877488/69‑1 (MQ=255)
aTCAAACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:2651832/69‑1 (MQ=255)
aTCAAACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:2555867/69‑1 (MQ=255)
aTCAAACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:2400640/69‑1 (MQ=255)
aTCAAACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:2349502/69‑1 (MQ=255)
aTCAAACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:1937830/69‑1 (MQ=255)
aTCAAACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:1908936/69‑1 (MQ=255)
aTCAAACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:1892160/69‑1 (MQ=255)
aTCAAACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:1890639/69‑1 (MQ=255)
   aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                          <  1:1008314/69‑1 (MQ=255)
   aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                          <  1:869301/69‑1 (MQ=255)
   aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                          <  1:1489990/69‑1 (MQ=255)
   aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                          <  1:1046324/69‑1 (MQ=255)
   aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                          <  1:3295490/69‑1 (MQ=255)
   aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                          <  1:2766302/69‑1 (MQ=255)
   aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                          <  1:1003979/69‑1 (MQ=255)
   aGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCt                                          <  1:1267906/69‑1 (MQ=255)
     aCCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCGATGCTCTCATgg                                        <  1:908837/69‑1 (MQ=255)
     aCCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATgg                                        <  1:1437801/69‑1 (MQ=255)
     aCCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATgg                                        <  1:1442107/69‑1 (MQ=255)
     aCCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATgg                                        <  1:498392/69‑1 (MQ=255)
     aCCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATgg                                        <  1:2954329/69‑1 (MQ=255)
     aCCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATgg                                        <  1:2500203/69‑1 (MQ=255)
      ccATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATgg                                        <  1:137622/68‑1 (MQ=255)
      ccATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGa                                       <  1:3274113/69‑1 (MQ=255)
      ccATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGa                                       <  1:2911980/69‑1 (MQ=255)
      ccATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGa                                       <  1:2730021/69‑1 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:1069082/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:2252848/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:1201063/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:2500819/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:2600194/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:265512/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:1614683/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:2822448/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:1732831/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:2945047/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:3211087/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:3335722/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:147628/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:1408603/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:203879/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:1729773/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:1892637/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:1850644/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:1993772/1‑69 (MQ=255)
           cTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:1806915/1‑69 (MQ=255)
           cTGGAGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATc                                  >  1:2079242/1‑69 (MQ=255)
                 cACTACGGTTATAAACTGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGc                            <  1:3185965/69‑1 (MQ=255)
                 cACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGc                            <  1:3240559/69‑1 (MQ=255)
                 cACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGc                            <  1:3236611/69‑1 (MQ=255)
                     aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        >  1:1144153/1‑69 (MQ=255)
                     aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        >  1:2384644/1‑69 (MQ=255)
                     aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        >  1:2600287/1‑69 (MQ=255)
                     aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        >  1:2628744/1‑69 (MQ=255)
                     aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        >  1:414058/1‑69 (MQ=255)
                     aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        >  1:1576353/1‑69 (MQ=255)
                     aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        >  1:509463/1‑69 (MQ=255)
                     aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        >  1:1293481/1‑69 (MQ=255)
                     aCGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGATCTCCTGGAATATCGACGGCCTGa                        >  1:1572591/1‑69 (MQ=255)
                     aCGGTTATAAACCGGAAATGGAGAAAGAACGCCTCGAATCCATGc                                                >  1:810953/1‑45 (MQ=255)
                                 cGGAAATGGAGCAAGAACGCCTCGAATCAATGctct                                             <  1:2967248/36‑1 (MQ=255)
                                     aaTGGCGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:2072095/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCTAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:2855905/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTGTCATGGAATATCGACGGCCTGATCCTCActg               >  1:2934031/1‑60 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACgg                             >  1:2164016/1‑48 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGt          >  1:270975/1‑67 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:2890563/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:1333670/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:2146787/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:64977/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:358722/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:1541996/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:1675452/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:1982351/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:1091167/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:1300651/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:1713326/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:1964037/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAATCAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGAACGTa         >  1:1811745/1‑68 (MQ=255)
                                     aaTGGAGCAAGAACGCCTCGAAACAATGCTCTCATGGAATATCGACGGCCTGATCCTCACTGa              >  1:855479/1‑63 (MQ=255)
                                       tGGAGGAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        >  1:1321937/1‑51 (MQ=255)
                                       tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        >  1:2013043/1‑51 (MQ=255)
                                       tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        <  1:2878295/51‑1 (MQ=255)
                                       tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        <  1:1681309/51‑1 (MQ=255)
                                       tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        >  1:2959998/1‑51 (MQ=255)
                                       tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        >  1:1789164/1‑51 (MQ=255)
                                       tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        <  1:3333409/51‑1 (MQ=255)
                                       tGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        >  1:1110091/1‑51 (MQ=255)
                                         gAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCcac    >  1:489796/1‑69 (MQ=255)
                                         gAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCcac    >  1:1748849/1‑69 (MQ=255)
                                         gAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCcac    >  1:3284195/1‑69 (MQ=255)
                                         gAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCcac    >  1:1988492/1‑69 (MQ=255)
                                         gAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCca     >  1:957664/1‑68 (MQ=255)
                                           gCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCacac  >  1:1441271/1‑69 (MQ=255)
                                                   gCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGa                        <  1:1040269/39‑1 (MQ=255)
                                                             |                                                  
ATCAGACCATGCTGGCGCACTACGGTTATAAACCGGAAATGGAGCAAGAACGCCTCGAATCCATGCTCTCCTGGAATATCGACGGCCTGATCCTCACCGAACGTACCCACAC  >  minE/2642649‑2642760

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A