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 1,502,847 A→T 52.3% intergenic (‑220/‑700) lrhA ← / → yfbQ DNA‑binding transcriptional repressor/predicted aminotransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,502,8470AT52.3% 11.0 / 120.6 86intergenic (‑220/‑700)lrhA/yfbQDNA‑binding transcriptional repressor/predicted aminotransferase
Reads supporting (aligned to +/- strand):  ref base A (18/23);  new base T (21/24);  total (39/47)
Fisher's exact test for biased strand distribution p-value = 8.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

ACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCACTC  >  minE/1502779‑1502916
                                                                    |                                                                     
acaTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATAACTTCAGGGATCGCATATCTATTAAGTTa                                                                     >  1:290752/1‑71 (MQ=255)
 caTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATac                                                                    >  1:3361709/1‑71 (MQ=255)
  aTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTact                                                                   <  1:2204028/71‑1 (MQ=255)
  aTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTact                                                                   >  1:125053/1‑71 (MQ=255)
  aTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATact                                                                   >  1:1647082/1‑71 (MQ=255)
  aTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATact                                                                   <  1:1260156/71‑1 (MQ=255)
  aTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATact                                                                   >  1:2594986/1‑71 (MQ=255)
  aTTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATact                                                                   <  1:1421115/71‑1 (MQ=255)
   ttGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATact                                                                   <  1:3049713/70‑1 (MQ=255)
   ttGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATact                                                                   >  1:1483142/1‑70 (MQ=255)
     gTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTactcac                                                                >  1:3662917/1‑71 (MQ=255)
      ttCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTactcact                                                               <  1:3646788/71‑1 (MQ=255)
         cGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCActct                                                             <  1:1806649/70‑1 (MQ=255)
         cGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCtt                                                            <  1:43923/71‑1 (MQ=255)
           ttATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCtttt                                                          <  1:3248270/71‑1 (MQ=255)
            tataATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCtttt                                                          <  1:3243611/70‑1 (MQ=255)
              taATGCCTGAAGTAGATCACAGAATATACCTTCAGGGATCGCATATCTATTAAGTTACTCActct                                                             <  1:1379056/65‑1 (MQ=255)
               aaTGCCTGAAGTAGATCACAAAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTAt                                                      >  1:3083605/1‑71 (MQ=255)
                aTGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAtt                                                     <  1:145020/71‑1 (MQ=255)
                 tGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTAttt                                                    <  1:1967258/71‑1 (MQ=255)
                 tGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTAtt                                                     >  1:1086128/1‑70 (MQ=255)
                   ccTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTAt                                                  <  1:887947/71‑1 (MQ=255)
                   ccTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTAt                                                  <  1:2050077/71‑1 (MQ=255)
                     tGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGa                                                >  1:2947886/1‑71 (MQ=255)
                      gAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGa                                                >  1:1069775/1‑70 (MQ=255)
                       aaGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCtttt                                                          >  1:3916375/1‑59 (MQ=255)
                       aaGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCt                                                        >  1:652395/1‑61 (MQ=255)
                       aaGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACa                                              >  1:3356718/1‑71 (MQ=255)
                          tAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATgc                                           >  1:3392364/1‑71 (MQ=255)
                          tAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCtttt                                                          <  1:2437684/56‑1 (MQ=255)
                            gATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTc                                                         <  1:736028/55‑1 (MQ=255)
                            gATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATgcgc                                         <  1:367657/71‑1 (MQ=255)
                              tCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATgcgc                                         >  1:1637024/1‑69 (MQ=255)
                              tCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATgcgc                                         >  1:1734473/1‑69 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGa                                                                       >  1:3629940/1‑38 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGa                                                                       >  1:3857459/1‑38 (MQ=255)
                               cacaGAATATATCTTCAGGGATCGCATATCTATTAAGATactcact                                                               >  1:2485460/1‑46 (MQ=255)
                                acaGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCgtgt                                     <  1:1614253/71‑1 (MQ=255)
                                acaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCtt                                                            <  1:1970371/48‑1 (MQ=255)
                                acaGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCgtgt                                     <  1:3354020/71‑1 (MQ=255)
                                 caGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGtt                                    <  1:2568727/71‑1 (MQ=255)
                                  aGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATgc                                           >  1:788554/1‑63 (MQ=255)
                                  aGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGttt                                   >  1:3162855/1‑71 (MQ=255)
                                   gAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCtt                                                            <  1:452683/45‑1 (MQ=255)
                                    aaTATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTAtt                                                     <  1:3274576/51‑1 (MQ=255)
                                    aaTATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTg                                  >  1:2616767/1‑70 (MQ=255)
                                    aaTATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGt                                 <  1:1289778/71‑1 (MQ=255)
                                    aaTATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGt                                 <  1:2220856/71‑1 (MQ=255)
                                      tatatCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtat                               <  1:3171883/71‑1 (MQ=255)
                                      tatatCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGta                                >  1:1159543/1‑70 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtata                              >  1:2760150/1‑70 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtat                               >  1:1819528/1‑69 (MQ=255)
                                        tatCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaa                             <  1:1789530/71‑1 (MQ=255)
                                         atCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAttt                                                    <  1:2790954/47‑1 (MQ=255)
                                         atCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAttt                                                    <  1:2740408/47‑1 (MQ=255)
                                          tCTTCAGGGATCGCATATCTATTAAGATACTCACTCtt                                                            <  1:3123407/38‑1 (MQ=255)
                                          tCTTCAGGGATCGCATATCTATTAAGATACTCACTCtt                                                            <  1:3143179/38‑1 (MQ=255)
                                            ttCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCt                                                        <  1:2487958/40‑1 (MQ=255)
                                            ttCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtat                               <  1:2325923/65‑1 (MQ=255)
                                              cAGCGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgta                        >  1:3533527/1‑70 (MQ=255)
                                               aGGGATCGCATATCTATTAAGATACTCACTCTTTTCTAt                                                      <  1:1337096/39‑1 (MQ=255)
                                               aGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaa                      >  1:1191432/1‑71 (MQ=255)
                                                gggATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaat                     <  1:2668933/71‑1 (MQ=255)
                                                gggATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaa                       <  1:978881/69‑1 (MQ=255)
                                                 ggATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATgc                                           >  1:483415/1‑48 (MQ=255)
                                                 ggATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatg                          >  1:3882551/1‑65 (MQ=255)
                                                  gATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:798779/71‑1 (MQ=255)
                                                  gATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:2759608/71‑1 (MQ=255)
                                                   aTCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:2368089/70‑1 (MQ=255)
                                                   aTCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaa                      <  1:3605950/67‑1 (MQ=255)
                                                    tCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATaaatgtaaatgt                   <  1:2492742/69‑1 (MQ=255)
                                                     cGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAg                >  1:877265/1‑71 (MQ=255)
                                                      gCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaa                       <  1:3048652/63‑1 (MQ=255)
                                                      gCATATCTACTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaatg                    <  1:282305/66‑1 (MQ=255)
                                                        atatCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTcc             >  1:3367362/1‑71 (MQ=255)
                                                         tatCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTAtaaatgtaaat                     <  1:1911610/62‑1 (MQ=255)
                                                         tatCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCt            >  1:2487772/1‑71 (MQ=255)
                                                         tatCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCt            >  1:2673168/1‑71 (MQ=255)
                                                          atCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCtt           >  1:2690856/1‑71 (MQ=255)
                                                           tCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGtat                               >  1:3112030/1‑50 (MQ=255)
                                                            cTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCgtgt                                     >  1:1154437/1‑43 (MQ=255)
                                                            cTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTg          >  1:2489608/1‑70 (MQ=255)
                                                             tATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGtt                                    >  1:3544273/1‑43 (MQ=255)
                                                              aTTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTc       >  1:2363355/1‑71 (MQ=255)
                                                               ttAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGta                                <  1:1056273/45‑1 (MQ=255)
                                                               ttAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTc       >  1:583819/1‑70 (MQ=255)
                                                                tAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGt         <  1:2681355/67‑1 (MQ=255)
                                                                   gATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCActc  <  1:3462036/71‑1 (MQ=255)
                                                                    |                                                                     
ACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGATACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTCCTTGTTCCACTC  >  minE/1502779‑1502916

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