Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913266,1490CT21.7% 98.8 / 21.7 46G135G (GGG→GGA) yafYCP4‑6 prophage; inner membrane lipoprotein YafY
Reads supporting (aligned to +/- strand):  ref base C (15/21);  new base T (7/3);  total (22/24)
Fisher's exact test for biased strand distribution p-value = 1.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.07e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CAGAGGCATTAAAGCTCGCGAGCAGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATAT  >  NC_000913/266021‑266288
                                                                                                                                |                                                                                                                                           
cAGAGGCATTAAAGCTCGCGAGCAGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGttt                                                                                                                                  <  1:482754/140‑1 (MQ=255)
     gCATTAAAGCTCGCGAGCAGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGt                                                                                                                             <  1:487801/140‑1 (MQ=255)
       aTTAAAGCTCGCGAGCAGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCa                                                                                                                           <  1:658564/140‑1 (MQ=255)
               tCGCGAGCAGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTa                                                                                                                   >  1:72986/1‑140 (MQ=255)
                  cgAGCAGTACACCCGACAGCATTAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTc                                                                                                                <  1:254120/140‑1 (MQ=255)
                            ccccGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTAtttt                                                                                                      <  1:398193/139‑1 (MQ=255)
                                gCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCtt                                                                                                  <  2:72986/140‑1 (MQ=255)
                                  cAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTg                                                                                                >  2:396674/1‑140 (MQ=255)
                                   aGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCTGTTTGCCCTCATGGGCCTACTACAAGTATTGTTCTTTgg                                                                                               >  2:360820/1‑140 (MQ=255)
                                   aGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCGGTTTGTCGTCATGGGCGTACTCAAAGTATTGTTCTTTgg                                                                                               >  2:330412/1‑140 (MQ=255)
                                   aGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTAATGGGCTTACTCAGAGTATTTTTCTTTgg                                                                                               >  1:360804/1‑140 (MQ=255)
                                     cATAAACCGACTTAGTGAAAGTATTGTCATGCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGta                                                                                             >  2:448460/1‑140 (MQ=255)
                                                ttAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGt                                                                                  <  1:464453/140‑1 (MQ=255)
                                                 tAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTc                                                                                 <  1:448460/140‑1 (MQ=255)
                                                  aGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGTCGTGCTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCa                                                                                >  2:297546/1‑140 (MQ=255)
                                                     gAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCAcct                                                                             <  1:464708/140‑1 (MQ=255)
                                                            ttGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTa                                                                      >  2:588297/1‑140 (MQ=255)
                                                              gTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTAtt                                                                    <  1:446564/140‑1 (MQ=255)
                                                                    cTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCa                                                                                <  2:529389/122‑1 (MQ=255)
                                                                    cTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCa                                                                                >  1:529389/1‑122 (MQ=255)
                                                                    cTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGtt                                                              >  1:707570/1‑140 (MQ=255)
                                                                             tttGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTAt                                                     <  1:130143/140‑1 (MQ=255)
                                                                             tttGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTAt                                                     <  2:443251/140‑1 (MQ=255)
                                                                             tttGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTAt                                                     <  2:287361/140‑1 (MQ=255)
                                                                             tttGTCGTTGTTTTACTCCTGACTGCCAGCGTTCGAGCGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTAt                                                     <  1:198320/140‑1 (MQ=25)
                                                                                     gtttttATTCCCGGTTATCAGGGTTTGACGGTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATa                                             <  1:480782/138‑1 (MQ=11)
                                                                                       ttttATTCCCGGTTATCAGGGTTTGACGGTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATaca                                           <  1:409998/140‑1 (MQ=11)
                                                                                        tttATTCCCGGTTATCAGGGTTTGACGGTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATacac                                          >  2:450793/1‑140 (MQ=11)
                                                                                         ttATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATAcaca                                         <  1:124235/140‑1 (MQ=255)
                                                                                           aTTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAgc                                       <  2:707570/140‑1 (MQ=255)
                                                                                               ccggttatCAGGGTTTGACGGTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCAt                                   <  1:30635/133‑1 (MQ=14)
                                                                                               cTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTTATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCCCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCAt                                   <  1:365539/140‑1 (MQ=255)
                                                                                                cggttatCAGGGTTTGACGGTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCAtt                                  >  2:557611/7‑140 (MQ=14)
                                                                                                  aTTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATtca                                >  2:498871/1‑140 (MQ=255)
                                                                                                    tGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATtcatc                              <  1:396674/140‑1 (MQ=255)
                                                                                                            tttgacggTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTg                      >  1:714379/7‑140 (MQ=14)
                                                                                                            ttCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTg                      >  2:113184/1‑140 (MQ=255)
                                                                                                             ttgacggTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTgg                     >  2:36889/6‑140 (MQ=14)
                                                                                                              tgacggTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGa                    >  1:75962/5‑140 (MQ=17)
                                                                                                                aGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACg                  >  2:597766/1‑140 (MQ=255)
                                                                                                                   gTATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGtt               >  1:419470/1‑140 (MQ=255)
                                                                                                                    tATCAGCAGCCGTCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGttt              >  1:392933/1‑140 (MQ=255)
                                                                                                                            gCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGc      <  2:670620/140‑1 (MQ=255)
                                                                                                                             cTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCa     <  1:498871/140‑1 (MQ=255)
                                                                                                                               gCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCata   >  1:139297/1‑140 (MQ=255)
                                                                                                                               gCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCCGCAATACACAGCACATACATCAGTGCCTGGGCGGTTTTTTCCTGCata   >  2:267591/1‑140 (MQ=21)
                                                                                                                                ccccATCAGTTTGCCTTCATGGTCGGACTCAAAGTATATTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCatat  <  1:360820/140‑1 (MQ=255)
                                                                                                                                ccccATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCatat  >  2:603161/1‑140 (MQ=255)
                                                                                                                                |                                                                                                                                           
CAGAGGCATTAAAGCTCGCGAGCAGTACACCCGCCAGCATAAACCGACTTAGTGAAAGTATTGTCATTCTTGTCTCCTTTGTCGTTGTTTTATTCCTGATTGTCAGGGTTCGAGGGTATCAGTAGCTGCCCCATCAGTTTGCCGTCATGGGCGTACTCAAAGTATTTTTCTTTGGTATACGGGTCCGTCACCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATAT  >  NC_000913/266021‑266288

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑