Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL60669,8900A→G10.6% 4.0 ‑6.5 ‑0.0721252araAL‑arabinose isomerase
Rejected: Prediction has biased read strand distribution supporting polymorphism.
Reads supporting (aligned to +/- strand):  new base (8/0):  ref base (26/38):  total (34/38)
Fisher's exact test strand distribution p-value = 1.52e-03
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 9.97e-01

CCACAGCGCATTCGCCACCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTCGATACAGTTAACCA  >  REL606/69855‑69925
                                   |                                   
ccACAGCGCATTCGCCACCGGCAGTTTCGGCAGGGa                                     <  1:2117590/36‑1 (MQ=255)
  acaGCGCATTCGCCACCGGCAGTTTCGGCAGGGAGt                                   <  1:230351/36‑1 (MQ=255)
   caGCGCATTCGCCACCGGCAGTTTCGGCATGGAGTg                                  <  1:6019318/36‑1 (MQ=255)
   caGCGCATTCGCCACCGGCAGTTTCGGCAGGGGGTg                                  >  1:649709/1‑36 (MQ=255)
   caGCGCATTCGCCACCGGCAGTTTCGGCAGGGAGTg                                  <  1:1265345/36‑1 (MQ=255)
    aGCGCGTTCGCCACCGGCAGTTTCGGCAGGGAGTGc                                 <  1:3944285/36‑1 (MQ=255)
    aGCGCATTCGCCACCGGCAGTTTCGGCAGGGAGTGc                                 <  1:6893561/36‑1 (MQ=255)
    aGCGCATTCGCCACCGGCAGTTTCGGCAGGGAGTGc                                 <  1:2948820/36‑1 (MQ=255)
     gcgcATTCGCCACCGGCAGTTTCGGCAGGGGGTGCg                                >  1:4403934/1‑36 (MQ=255)
      cgcATTCGCCACCGGCAGGTTCGGCAGGGAGGGCgg                               >  1:6269626/1‑36 (MQ=37)
       gcATTCGCCACCGGCAGTTTCGGCAGGGGGTGGggg                              >  1:3908338/1‑35 (MQ=37)
       gcATTCGCCACCGGCAGTTTCGGCAGGGGGTGGGgt                              >  1:7044965/1‑36 (MQ=37)
       gcATTCGCCACCGGCAGTTTCGGCAGGGAGTGCGgt                              <  1:303940/36‑1 (MQ=255)
       gcATTCGCCACCGGCAGTTTCGGCAGGGAGTGCGgt                              <  1:3089633/36‑1 (MQ=255)
       gcATTCGCCACCGGCAGTTTCAGCAGGGAGTGCGgt                              <  1:3391142/36‑1 (MQ=255)
       gcATTCGCCACCGGCAGGTTCGTCCGGGGGTACggg                              >  1:6398776/1‑35 (MQ=9)
        cATTCGCCACCGGCAGTTTCGGCCGGGGGTGCgggg                             >  1:1806390/1‑34 (MQ=25)
        cATTCGCCACCGGCAGTTTCGGCAGGGAGGGCGgtg                             >  1:6090960/1‑36 (MQ=255)
           tCGCCACCGGCAGTTTCTGCAGGGAGTGGGgggtgt                          >  1:6085955/1‑34 (MQ=18)
           tCGCCACCGGCAGTTTCGGCAGGGAGTGCGGTGttt                          <  1:3036640/36‑1 (MQ=255)
           tCGCCACCGGCAGTTTCGGCAGGGAGTGCGGTGttt                          <  1:4545479/36‑1 (MQ=255)
             gCCACCGGCAGTTTCGGCCGGGGGGGCGGGGgtttt                        >  1:3991178/1‑35 (MQ=12)
             gCCACCGGCAGTTTCGGCAGGGGGGGGGGTGTTTTc                        >  1:6321655/1‑36 (MQ=25)
             gCCACCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTc                        <  1:2710674/36‑1 (MQ=255)
              ccACCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCa                       <  1:6512360/36‑1 (MQ=255)
              ccACCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCa                       <  1:953594/36‑1 (MQ=255)
               ccccGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCAc                      <  1:3264109/34‑1 (MQ=255)
               cACCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTTAc                      >  1:2275593/1‑36 (MQ=255)
               cACCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCAc                      <  1:6321542/36‑1 (MQ=255)
               cACCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCAc                      <  1:3256109/36‑1 (MQ=255)
                aCCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCAcc                     <  1:5406209/36‑1 (MQ=255)
                 ccGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCACCg                    >  1:1477601/1‑36 (MQ=255)
                  cGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCACCgt                   <  1:4318094/36‑1 (MQ=255)
                   ggCAGTTTCGGCAGGGAGTGCGGTGTTTTCACCgtg                  >  1:7206182/1‑36 (MQ=255)
                    gCAGTTTCGGCAGGGAGTGCGGTGTTTTCACCgtgt                 >  1:4730592/1‑36 (MQ=255)
                    gCAGTTTCGGCAGGGAGTGCGGTGTTTTCACCgtgt                 <  1:1897593/36‑1 (MQ=255)
                    gCAGTTTCGGCAGGGAGTGCGGTGTTTTCACCgtgt                 <  1:5542284/36‑1 (MQ=255)
                    gCAGTTTCGGCAGGGAGTGCGGGGTTTTCACCgtgt                 >  1:3022770/1‑36 (MQ=255)
                    gCAGTTTCGGCAGGGAATGCGGTGTTTTCACCgtgt                 >  1:4735836/1‑36 (MQ=255)
                     cAGTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTc                <  1:5069563/36‑1 (MQ=255)
                     cAGTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTc                >  1:7706050/1‑36 (MQ=255)
                     cAGTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTc                <  1:1857252/36‑1 (MQ=255)
                     cAGTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTc                <  1:5465185/36‑1 (MQ=255)
                      aGTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTCg               <  1:3688133/36‑1 (MQ=255)
                      aGTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTCg               <  1:4524132/36‑1 (MQ=255)
                      aGTTTCGGCAGGGAGTGCGGTGTTTTCAACgtgtgg               >  1:106215/1‑34 (MQ=38)
                       gTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTCGa              >  1:1127101/1‑36 (MQ=255)
                       gTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTCGa              >  1:1756390/1‑36 (MQ=255)
                       gTTTCGGCAGGGAGGGCGGTGTTTTCTCCGTGTCGa              >  1:4305762/1‑36 (MQ=37)
                         ttCGGCAGGGAGTGCGGTGTTTTCACCGTGTCGATa            >  1:4090480/1‑36 (MQ=255)
                         ttCGGCAGGGAGTGCGGTGTTTTCACCGTGTCGATa            <  1:3508247/36‑1 (MQ=255)
                           cGGCAGGGAGTGCGGTGTTTTCACCGTGTCGATACa          >  1:4689916/1‑36 (MQ=255)
                            ggCAGGGAGTGCGGTGTTTTCACCGTGTCGATACAg         >  1:2158390/1‑36 (MQ=255)
                            ggCAGGGAGTGCGGTGTTTTCACCGTGTCGATACAg         <  1:2528604/36‑1 (MQ=255)
                            ggCAGGGAGTGCGGTGTTTTCACCGTGTCGATAAAg         >  1:7748453/1‑36 (MQ=255)
                             gCAGGGAGTGCGGTGTTTTCACCGTGTCGATACAGt        <  1:1271143/36‑1 (MQ=255)
                             gCAGGGAGTGCGGTGTTTTCACCGTGTCGATACAGt        >  1:5385993/1‑36 (MQ=255)
                             gCAGGGAGTGCGGTGTTTTCACCGTGTCGATACAGt        >  1:303489/1‑36 (MQ=255)
                             gCAGGGAGTGCGGTGTTTTCACCGTGTCGATACAGt        >  1:214064/1‑36 (MQ=255)
                             gCAGGGAGTGCGGTGTTTTCACCGTGTCGATACAGt        <  1:3788274/36‑1 (MQ=255)
                              cAGGGAGTGCGGTGTTTTCACCGTGTCGATACAGtt       <  1:5793298/36‑1 (MQ=255)
                              cAGGGAGTGCGGTGTTTTCACCGTGTAGATACAGtt       >  1:7076514/1‑36 (MQ=255)
                               tgggAGTGCGGTGTTTTCACCGTGTCGATACAGTTa      <  1:193487/35‑1 (MQ=255)
                               aGGGAGTGCGGTGTTTTGACCGTGTTGATACAGCTa      >  1:5712892/1‑36 (MQ=25)
                               aGGGAGTGCGGTGTTTTCACCGTGTCGATACAGTTa      <  1:3356220/36‑1 (MQ=255)
                               aGGGAGTGCGGTGTTTTCACCGTGTCGATACAGTTa      >  1:666975/1‑36 (MQ=255)
                               aGGGAGTGCGGTGTTTTCACCGTGTCGATACAGTTa      >  1:1365072/1‑36 (MQ=255)
                               aGGGAGTGCGGTGTTTTCACCGTGTCGATACAGTTa      <  1:5106246/36‑1 (MQ=255)
                                gagAGTGCGGTGTTTTCACCGTGTCGATACAGTTaa     <  1:4586458/34‑1 (MQ=255)
                                 ggAGTGCGGTGTTTTCACCGTGTCGATACAGTTAAc    >  1:1683962/1‑36 (MQ=255)
                                 ggAGTGCGGTGTTTTCACCGTGTCGATACAGTTAAc    <  1:319740/36‑1 (MQ=255)
                                 ggAGTGCGGTGTTTTCACCGTGTCGATACAGTTAAc    <  1:286394/36‑1 (MQ=255)
                                  gAGTGCGGTGTTTTCACCGTGTCGATACAGTTAAcc   <  1:101419/36‑1 (MQ=255)
                                   aGTGCGGTGTTTTCACCGTGTCGATACAGTTAACca  <  1:6510458/36‑1 (MQ=255)
                                   aGTGCGGTGTTTTCACCGTGTCGATACAGTTAACca  <  1:2727814/36‑1 (MQ=255)
                                   aGTGCGGTGTTTTCACCGTGTCGATACAGTTAACca  >  1:1675720/1‑36 (MQ=255)
                                   aGTGCGGTGTTTTCACCGTGTCGATACAGTTAACca  >  1:297719/1‑36 (MQ=255)
                                   |                                   
CCACAGCGCATTCGCCACCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTCGATACAGTTAACCA  >  REL606/69855‑69925

Base quality scores:  ATCG  < 3 ≤  ATCG  < 7 ≤  ATCG  < 20 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG