Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,632,5230AC30.8% 97.2 / 16.3 52intergenic (‑238/‑367)ydfJ/ynfTputative transporter YdfJ/Qin prophage; protein YnfT
Reads supporting (aligned to +/- strand):  ref base A (19/17);  new base C (0/16);  total (19/33)
Fisher's exact test for biased strand distribution p-value = 1.27e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

ATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCAGATACATCAC  >  NC_000913/1632466‑1632590
                                                         |                                                                   
aTGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATc                                                           <  1:283946/68‑1 (MQ=255)
 tGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCg                                                          >  1:3336686/1‑68 (MQ=255)
 tGCGTAAAATCAAGAACGGCTGGAAATCATTCAACACTCACACTATCGAAAAATTTACCAGCCAATCg                                                          >  1:3168033/1‑68 (MQ=255)
   cGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCgca                                                        <  1:262155/68‑1 (MQ=255)
   cGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACTACCGAAAAATTTCCCAGCCAATCgca                                                        <  1:1236442/68‑1 (MQ=255)
   cGTAAAATCAAGAACGGCTGGAAATCATTCAATACCCACACTATCGAAAAATTTCCCAGCCAATCgca                                                        <  1:2195216/68‑1 (MQ=255)
   cGTAAAATCAAGAACGGCGGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCgca                                                        <  1:521380/68‑1 (MQ=255)
    gTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCgcag                                                       >  1:3666075/1‑68 (MQ=255)
     tAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTCCCAGCCAATCgcagc                                                      <  1:1927271/68‑1 (MQ=255)
        aaTCAAGAGCGGCTGGAAATCATTCAATACTCACCCTATCGAAAAATTTCCCAGCCAATCGCAGCACg                                                   <  1:3426964/68‑1 (MQ=21)
         ataaaGAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGt                                                  <  1:2742445/65‑1 (MQ=255)
         aTCAAGAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTCCCAGCCAATCGCAGCACGt                                                  <  1:3518226/68‑1 (MQ=255)
         aTCAAGAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGt                                                  <  1:2742471/68‑1 (MQ=255)
          tcgaGAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGtt                                                 <  1:3213937/65‑1 (MQ=255)
          tCAATAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGtt                                                 <  1:4031505/68‑1 (MQ=255)
          tCAAGAACGTGTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGtt                                                 <  1:4148324/68‑1 (MQ=255)
          tCAAGAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGtt                                                 <  1:2560580/68‑1 (MQ=255)
          tCAAGAACGGCTGGAAATCATTCAATACTCACACTATCAAAAATTTTCCCAGCCAATCGCAGCACGtt                                                 <  1:3147231/68‑1 (MQ=21)
          tCAAGAACGCCTGGAAATCATTCAATCCTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGtt                                                 <  1:4164317/68‑1 (MQ=255)
          tCAAAAACGGCTGGAAATCTTTCAATACTCCCACTATCGAAAAATTTCCCAGCCAATCGCAGCACGtt                                                 <  1:4034194/68‑1 (MQ=21)
          ccAAGAGCGCCTGGAAATCATTCAATCCCCACACTAACAAAAAATTTACCAGCCAATCGCAGCACGtt                                                 <  1:1249056/67‑1 (MQ=25)
            aaGAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCt                                               <  1:1548549/68‑1 (MQ=255)
              gAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTCCCAGCCAATCGCAGCACNTTCTTg                                             <  1:2450878/68‑1 (MQ=255)
              gAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTCCCAGCCAATCGCAGCACGTTCTTg                                             <  1:144112/68‑1 (MQ=255)
              gAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTg                                             >  1:176938/1‑68 (MQ=255)
              aaaCGGCTGAAAATCATTCAATACTCACCCTATCGAAAAATTTCCCAGCCAATCGCAGCACGTTCTTg                                             <  1:730493/67‑1 (MQ=18)
                gctgCTGGAATGCTTACAATTCACACACTATCGAAAATTTGACCAGCCAATCGCAGCACGTTCTTGCa                                           <  1:1226645/65‑1 (MQ=19)
                aCGGCTGGAAATCATTCAATCCGCACACTACCGAAAAATTTCCCAGCCAATCGCAGCACGTTCTTGCa                                           <  1:2768649/68‑1 (MQ=21)
                aCGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTCCCAGCCAATCGCAGCACGTTCTTGCa                                           <  1:3568710/68‑1 (MQ=255)
                aCGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTCCCAGCCAATCGCAGCACGTTCTTGCa                                           <  1:136063/68‑1 (MQ=255)
                aCGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCa                                           >  1:169510/1‑68 (MQ=255)
                aCGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTCGCa                                           >  1:1682769/1‑68 (MQ=255)
                aCGGCTGGAAATCATTCAATACTCACACTATCAAAAAATTTACCAGCCAATCGCAGCACGTNCTTGCa                                           <  1:2448954/68‑1 (MQ=255)
                aCGGCTGAAAATCATTCAATACTCACACTATCGAAAAATTTCCCAGCCAATCGCAGCACGTTCTTGCa                                           <  1:1955380/68‑1 (MQ=255)
                    cTGGAAATCATTCGATACTCACACTATCGAAAAATTTCCCAGCCAATCGCAGCACGTTCTTGCATAAg                                       <  1:3074819/68‑1 (MQ=21)
                    cTGGAAATCATTCAATCCTCACACTATCGAAAAATTTCCCAGCCAATCGCAGCACGTTCTTGCATAAg                                       <  1:1935672/68‑1 (MQ=21)
                    cTGGAAATCATTCAATACTCCCACTATCGAAAAATTTCCCAGCCAATCGCAGCACGTTCTTGCATAAg                                       <  1:3650732/68‑1 (MQ=21)
                    cTGGAAATCATTCAATACTCACACTATCGAAAATTTTACCAGCCAATCGCAGCACGTTCTTGCATAAg                                       <  1:2704892/68‑1 (MQ=255)
                    cTGGAAATCATTCAATACTCACACTATCGAAAAATTTCCCAGCCAATCGCAGCACGTTCTTGCATAAg                                       <  1:3659253/68‑1 (MQ=255)
                    cTGGAAATCATTCAATACTCACACTATCGAAAAATTTCCCAGCCAATCGCAGCACGTTCTTGCATAAg                                       <  1:2703441/68‑1 (MQ=255)
                    cTGGAAATCATTCAATACTCACACTATCGAAAAATTTCCCAGCCAATCGCAGCACGTTCTTGCATAAg                                       <  1:801673/68‑1 (MQ=255)
                    cTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAg                                       <  1:239424/68‑1 (MQ=255)
                     tgaaaaTCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAgg                                      <  1:169468/65‑1 (MQ=255)
                      ggAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGgt                                     <  1:3804928/68‑1 (MQ=255)
                          aTCATTCAGTACTCCCTCTATCAAAAAATTGACCAGCCAATCGCAGCACGTTCTTGCATAAGgtgtgt                                 <  1:1580853/68‑1 (MQ=37)
                          aTCATTCAATACTCACGCTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGgtatgt                                 >  1:2732781/1‑68 (MQ=255)
                          aTCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGgtgtgt                                 >  1:2272017/1‑68 (MQ=255)
                          aTCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGgtgtgt                                 >  1:344395/1‑68 (MQ=255)
                          aTCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGgtgtgt                                 >  1:120287/1‑68 (MQ=255)
                               tCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCg                            >  1:853419/1‑68 (MQ=255)
                                  aTACTCCCACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGtt                         <  1:386020/68‑1 (MQ=255)
                                  aTACTCACCCGATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGtt                         <  1:3705050/68‑1 (MQ=255)
                                  aTACTCACACTATCGAAAAATTTCCCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGtt                         <  1:1060781/68‑1 (MQ=255)
                                  aTACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGtt                         >  1:3963191/1‑68 (MQ=255)
                                  aTACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGtt                         <  1:1553629/68‑1 (MQ=255)
                                   tACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGttt                        >  1:9001/1‑68 (MQ=255)
                                   tACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGttt                        <  1:4055190/68‑1 (MQ=255)
                                    aCTCACACTATCGAAAAATTTATCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGtttt                       >  1:3175676/1‑68 (MQ=255)
                                    aCTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGtttt                       >  1:2910416/1‑68 (MQ=255)
                                    aCTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGtttt                       >  1:2102475/1‑68 (MQ=255)
                                       cacaCTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCa                    <  1:760510/68‑1 (MQ=255)
                                         cacTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAAc                  >  1:4110478/1‑68 (MQ=255)
                                         cacTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAAc                  >  1:3042106/1‑68 (MQ=255)
                                         cacTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGAGTGTCTGCGGTTTTTCAAc                  >  1:3919466/1‑68 (MQ=255)
                                            tATCGAAAATTTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTAt               <  1:1121428/68‑1 (MQ=255)
                                            tATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTAt               <  1:217458/68‑1 (MQ=255)
                                            tATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTAt               <  1:3762840/68‑1 (MQ=255)
                                            tATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTAt               <  1:3075936/68‑1 (MQ=255)
                                            tATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTAt               <  1:2014205/68‑1 (MQ=255)
                                            tATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTAt               <  1:503152/68‑1 (MQ=255)
                                             aTCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTAtt              <  1:248010/68‑1 (MQ=255)
                                              tCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTc             <  1:1672516/68‑1 (MQ=255)
                                               cGAAGAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCa            <  1:3658185/68‑1 (MQ=255)
                                                gAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCAg           >  1:1908494/1‑68 (MQ=255)
                                                 aaagaTTTACCAGCCGATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCAGa          <  1:3944623/68‑1 (MQ=255)
                                                 aaaaaTTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCAGa          <  1:1657429/68‑1 (MQ=255)
                                                  aaaaTTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCAGAt         >  1:3521074/1‑68 (MQ=255)
                                                    aaTTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCAGATAc       >  1:4124012/1‑68 (MQ=255)
                                                    aaTTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCAGATAc       >  1:1704250/1‑68 (MQ=255)
                                                    aaTTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCAGATAc       <  1:4094569/68‑1 (MQ=255)
                                                     aTTTACCGGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCAGATACa      <  1:2555470/68‑1 (MQ=255)
                                                     aTTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCAGATACa      <  1:3885164/68‑1 (MQ=255)
                                                     aTTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCAGATACa      <  1:2989869/68‑1 (MQ=255)
                                                         aCCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCAGATACATCAc  <  1:1632689/68‑1 (MQ=255)
                                                         |                                                                   
ATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACTATCGAAAAATTTACCAGCCAATCGCAGCACGTTCTTGCATAAGGTGTGTCTGCGGTTTTTCAACTATTCAGATACATCAC  >  NC_000913/1632466‑1632590

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑