Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6062,732,3200G→C 4.9% 6.2 ‑14.9 ‑0.0222intergenic (‑35/+118)hypF/hydNcarbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases/formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
Rejected: Polymorphism prediction not supported by minimum number of reads on both strands.
Rejected: Prediction has biased read strand distribution supporting polymorphism.
Rejected: Polymorphic base substitution creates a homopolymer stretch.
Reads supporting (aligned to +/- strand):  new base (0/12):  ref base (154/56):  total (154/68)
Fisher's exact test strand distribution p-value = 3.29e-07
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 9.99e-01

Only 100 of 249 total aligned reads displayed.

TGAATTATTCCCGCCATCATGAATTGCGTAACCCGCCCAGCCGGACACGACAGCGTCGCATCCGGTAGT  >  REL606/2732286‑2732354
                                  |                                  
tGAATTATTCCCGCCATCATGAATTGCGTAACCCg                                    <  1:9962019/35‑1 (MQ=255)
tGAATTATTCCCGCCATCATGAATTGCGTAACCCg                                    <  1:16999918/35‑1 (MQ=255)
tGAATTATTCCCGCCATCATGAATTGCGTAACACg                                    <  1:20335240/35‑1 (MQ=255)
 gAATTATTCCCGCCTTCATGAATTGCGTAACCCGc                                   <  1:18580214/35‑1 (MQ=255)
 gAATTATTCCCGCCATCATGAATTGCGTAACCCGc                                   >  1:16568704/1‑35 (MQ=255)
 gAATTATTCCCGCCATCATGAATTGCGTAACCCGc                                   >  1:15010284/1‑35 (MQ=255)
  atttatcCCCGCCATCATGAATTGCGTAACCCGcc                                  <  1:8994414/33‑1 (MQ=38)
  aaTTATTCCCGCCATCATGAATTGCGTAACCCGcc                                  >  1:16441394/1‑35 (MQ=255)
  aaTTATTCCCGCCATCATGAATTGCGTAACCCGcc                                  >  1:1627496/1‑35 (MQ=255)
  aaTTATTCCCGCAATCATGAATTGCGTAACACGcc                                  <  1:19440325/35‑1 (MQ=37)
  aaTTATCCCCGCCATCATGAATTGCGTAACCCGcc                                  <  1:17145684/35‑1 (MQ=255)
  aaTTATCCCCGCCATCATGAATTGCGTAACCCGcc                                  <  1:10498343/35‑1 (MQ=255)
   attattCCCGCCATCATGAATTGCGTAACCCGccc                                 <  1:15576530/35‑1 (MQ=255)
   attattCCCGCCATCATGAATTGCGTAACCCGccc                                 <  1:2559051/35‑1 (MQ=255)
   attattCCCGCCATCATGAATTGCGTAACCCGccc                                 <  1:8479056/35‑1 (MQ=255)
   attattCCCGCCATCATGAATTGCGTAACCCGccc                                 <  1:8083439/35‑1 (MQ=255)
   attattCCCGCCATCATGAATTGCGTAACCCGccc                                 >  1:11718286/1‑35 (MQ=255)
   attatcCCCGCCATCATGAATTGCGTAACCCGccc                                 <  1:1941472/35‑1 (MQ=255)
    ttattCCCGCCATCATGAATTGCGTAACCCGCCCa                                >  1:18734499/1‑35 (MQ=255)
    ttattCCCGCCATCATGAATTGCGTAACCCGCCCa                                <  1:4569070/35‑1 (MQ=255)
    ttattCCCGCCATCATGAATTGCGTAACCCGCCCa                                <  1:3194699/35‑1 (MQ=255)
    ttattCCCGCCATCATGAATTGCGTAACCCGCCCa                                >  1:13726744/1‑35 (MQ=255)
    ttattCCCGCCATCATGAATTGCGTAACCCGCCCa                                >  1:71546/1‑35 (MQ=255)
    ttatcCCCGCCATCATGAATTGCGTAACCCGCCCa                                <  1:18058689/35‑1 (MQ=255)
     tattCCCGCCATCATGAATTGCGTAACCCGCCCAg                               >  1:16807116/1‑35 (MQ=255)
     tattCCCGCCATCATGAATTGCGTAACCCGCCCAg                               <  1:3002576/35‑1 (MQ=255)
     tattCCCGCCATCATGAATTGCGTAACCCGCCCAg                               >  1:17722257/1‑35 (MQ=255)
     tattCCCGCCATCATGAATTGCGTAACCCGCACAg                               <  1:10164278/35‑1 (MQ=255)
      attCCCGCCATCATGAATTGCGTAACCCGCCCAGc                              >  1:6847527/1‑35 (MQ=255)
      attCCCGCCATCATGAATTGCGTAACCCGCCCAGc                              >  1:19319863/1‑35 (MQ=255)
       ttCCCCCCATCATTAATTGCGTAACCCGCCCAGcc                             >  1:568292/1‑35 (MQ=25)
       tccccCCCATCATGAATTGCGTAACCCGCCCAGcc                             <  1:13128578/33‑1 (MQ=38)
        tCCCGCCATCATGAATTGCGTAACCCGCCCAGCCg                            >  1:7133098/1‑35 (MQ=255)
        tCCCGCCATCATGAATTGCGTAACCCGCCCAGCCg                            >  1:12972939/1‑35 (MQ=255)
         cccGCCATCATGAATTGCGTAACCCGCCCAGCCgg                           >  1:15228060/1‑35 (MQ=255)
         cccGCCATCATGAATTGCGTAACCCGCCCAGCCgg                           >  1:10919435/1‑35 (MQ=255)
          ccGCCATCATGAATTGCGTACCCCCCCCAGCCGGa                          <  1:16595110/35‑1 (MQ=38)
          ccGCCATCATGAATTGCGTAACCCGCCCAGCCGGa                          >  1:19769398/1‑35 (MQ=255)
          ccGCCATCATGAATTGCGTAACCCGCCCAGCCGGa                          >  1:6735174/1‑35 (MQ=255)
          ccGCCATCATGAATTGCGTAACCCGCCCAGCCGGa                          >  1:7522921/1‑35 (MQ=255)
           cGCCATCATGAATTGCGTAACCCGCCCAGCCGGac                         >  1:10106694/1‑35 (MQ=255)
           cGCCATCATGAATTGCGTAACCCGCCCAGCCGGac                         >  1:19972539/1‑35 (MQ=255)
           cGCCATCATGAATTGCGTAACCCGCCCAGCCGGac                         <  1:8883947/35‑1 (MQ=255)
            gCCATCATGAATTGCGTAACCCGCCCAGCCGGaca                        >  1:7406610/1‑35 (MQ=255)
            gCCATCATGAATTGCGTAACCCGCCCAGCCGGaca                        >  1:8741436/1‑35 (MQ=255)
            gCCATCATGAATTGCGTAACCCGCCCAGCCGGaca                        >  1:2011903/1‑35 (MQ=255)
             ccATCATGAATTGCGTACCCCGCCCAGCCGGacac                       <  1:14043381/35‑1 (MQ=255)
             ccATCATGAATTGCGTAACCCGCCCAGCCGGacac                       >  1:6165587/1‑35 (MQ=255)
             ccATCATGAATTGCGTAACCCGCCCAGCCGGacac                       >  1:13224747/1‑35 (MQ=255)
             ccATCATGAATTGCGTAACCCGCCCAGCCGGacac                       >  1:6313886/1‑35 (MQ=255)
               atcatGAATTGCGTAACCCGCCCAGCCGGACACGa                     >  1:18379419/1‑35 (MQ=255)
               atcatGAATTGCGTAACCCGCCCAGCCGGACACGa                     <  1:5127225/35‑1 (MQ=255)
                tcatGAATTGCGTAACCCGCCCAGCCGGACACGAc                    <  1:3266160/35‑1 (MQ=255)
                tcatGAATTGCGTAACCCGCCCAGCCGGACACGAc                    >  1:4804819/1‑35 (MQ=255)
                tcatGAATTGCGTAACCCGCCCAGCCGGACACGAc                    >  1:16111705/1‑35 (MQ=255)
                 catGAATTGCGTAACCCGCCCAGCCGGACACGACa                   >  1:1962266/1‑35 (MQ=255)
                 catGAATTGCGTAACCCGCCCAGCCGGACACGACa                   >  1:9752949/1‑35 (MQ=255)
                 catGAATTGCGTAACCCGCCCAGCCGGACACGACa                   >  1:17623451/1‑35 (MQ=255)
                  atGAATTGCGTAACCCGCCCAGCCGGACACGACAg                  <  1:19006567/35‑1 (MQ=255)
                  atGAATTGCGTAACCCGCCCAGCCGGACACGACAg                  >  1:13604794/1‑35 (MQ=255)
                  atGAATTGCGTAACCCGCCCAGCCGGACACGACAg                  >  1:9922241/1‑35 (MQ=255)
                   tGAATTGTGTACCCCGCCCAGCCGGACACGACAGc                 <  1:787066/35‑1 (MQ=37)
                   tGAATTGCGTAACCCGCCCAGCCGGACACGATAGc                 >  1:14801897/1‑35 (MQ=255)
                   tGAATTGCGTAACCCGCCCAGCCGGACACGACAGc                 >  1:7964989/1‑35 (MQ=255)
                   tGAATTGCGTAACCCGCCCAGCCGGACACGACAGc                 >  1:8940966/1‑35 (MQ=255)
                   tGAATTGCGTAACCCGCCCAGCCGGACACGACAGc                 >  1:17406961/1‑35 (MQ=255)
                   tGAATTCCGTACCCCCCCCAGCCGGACACGACAGc                 <  1:5926881/35‑1 (MQ=25)
                    gAATTGCGTAACCCGCCCAGCCGGACACGACAGCg                >  1:6433731/1‑35 (MQ=255)
                     aaTTGCGTCCCCCCCCCAGCCGGACACGACAGCGt               <  1:5551916/35‑1 (MQ=25)
                     aaTTGCGTAACCCGCCCAGCCGGACACGACAGCGt               >  1:3330424/1‑35 (MQ=255)
                     aaTTGCGTAACCCGCCCAGCCGGACACGACAGCGt               >  1:4180012/1‑35 (MQ=255)
                     aaTTGCGTAACCCGCCCAGCCGGACACGACAGCGt               >  1:8262357/1‑35 (MQ=255)
                     aaTTGCGTAACCCGCCCAGCCGGACACGACAGCGt               >  1:5290083/1‑35 (MQ=255)
                      tttGCGTACCCCCCCCAGCCGGACACGACAGCGTc              <  1:3917851/34‑1 (MQ=37)
                      aTTGCGTAACCCGCCCAGCCGGACACGACAGCGTc              >  1:18194849/1‑35 (MQ=255)
                       ttGCGTAACCCGCCCAGCCGGACACGACAGCGTCg             >  1:10014530/1‑35 (MQ=255)
                       ttGCGTAACCCGCCCAGCCGGACACGACAGCGTCg             >  1:12501171/1‑35 (MQ=255)
                       ttGCGTAACCCGCCCAGCCGGACACGACAGCGTCg             >  1:14744135/1‑35 (MQ=255)
                       ttGCGTAACCCGCCCAGCCGGACACGACAGCGTCg             >  1:8847338/1‑35 (MQ=255)
                       ttGCGTAACCCGCCCAGCCGGACACGACAGCGTCg             >  1:20475467/1‑35 (MQ=255)
                        tGCTTACCCCCCCCAGCCGGACACGACAGCGTCGc            <  1:2668691/35‑1 (MQ=25)
                        tGCGTAACCCGCCCAGCCGGACACGACAGCGTCGc            >  1:6356688/1‑35 (MQ=255)
                        tGCGAACCCCCCCCAGCCGGACACGACAGCGTCGc            <  1:9603710/35‑1 (MQ=25)
                         gCGTAACCCGCCCAGCCGGACACGACAGCGTCGCa           >  1:9054860/1‑35 (MQ=255)
                          cGTAACCCGCCCAGCCGGACACGACAGCGTCGCAt          >  1:10277355/1‑35 (MQ=255)
                          cGTAACCCGCCCAGCAGGACACGACAGCGTCGCAt          <  1:15419998/35‑1 (MQ=255)
                           gTACCCCCCCCAGCCGGACACGACAGCGTCGCATc         <  1:4891210/35‑1 (MQ=25)
                           gTACCCCCCCCAGCCGGACACGACAGCGTCGCATc         <  1:7677382/35‑1 (MQ=25)
                           gTAACCCGCCCAGCCGGACACGACAGCGTCGCATc         >  1:15996071/1‑35 (MQ=255)
                           gTAACCCGCCCAGCCGGACACGACAGCGTCGCATc         >  1:11937519/1‑35 (MQ=255)
                           gTAACCCGCCCAGCCGGACACGACAGCGTCGCATc         >  1:12761401/1‑35 (MQ=255)
                            taccccCCCCAGCCGGACACGACAGCGTCGCATcc        <  1:5061737/32‑1 (MQ=25)
                             aaCCCGCCCAGCCGGACACGACAGCGTCGCATCCg       >  1:2077375/1‑35 (MQ=255)
                             aaCCCGCCCAGCCGGACACGACAGCGTCGCATCCg       >  1:10654222/1‑35 (MQ=255)
                             aaCCCGCCCAGCCGGACACGACAGCGTCGCATCCg       >  1:11233004/1‑35 (MQ=255)
                             aaCCCGCCCAGCCGGACACGACAGCGTCGCATCCg       >  1:11486855/1‑35 (MQ=255)
                              aCCCGCCCAGCCGGACACGACAGCGTCGCATCCgg      >  1:11124399/1‑35 (MQ=255)
                                ccGCCCAGCCGGACACGACAGCGTCGCATCCGGTa    >  1:1915410/1‑35 (MQ=255)
                                 cGCCCAGCCGGACACGACAGCGTCGCATCCGGTAg   >  1:14301226/1‑35 (MQ=255)
                                  gCCCAGCCGGACACGACAGCGTCGCATCCGGTAGt  >  1:4013313/1‑35 (MQ=255)
                                  |                                  
TGAATTATTCCCGCCATCATGAATTGCGTAACCCGCCCAGCCGGACACGACAGCGTCGCATCCGGTAGT  >  REL606/2732286‑2732354

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: 
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.