Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913732,9740GA21.9% 80.2 / 14.6 41S1131N (AGC→AAC) rhsCrhs element protein RhsC
Reads supporting (aligned to +/- strand):  ref base G (16/16);  new base A (5/4);  total (21/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.38e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACCTG  >  NC_000913/732844‑733110
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aGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGa                                                                                                                                 <  1:134365/140‑1 (MQ=35)
    tggtgTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGATAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGGCATGTGGACCCg                                                                                                                             >  2:455316/1‑140 (MQ=255)
    tggtgTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCg                                                                                                                             >  1:607903/1‑140 (MQ=34)
            ccgccgGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATacac                                                                                                                     >  1:139050/1‑140 (MQ=37)
            ccgccgGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGATGGCGCATATGTAATGCCAGACGGACCCGGTATacac                                                                                                                     >  1:341443/1‑140 (MQ=11)
              gccgGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGc                                                                                                                   >  1:142124/1‑140 (MQ=37)
                   tGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGgcg                                                                                                              >  2:399290/1‑140 (MQ=37)
                     cTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGAAGGTGGCGCTGATGCAAAGCCAGATGGACCCCGTATACACGCCGGcgcg                                                                                                            >  2:298234/1‑140 (MQ=255)
                     cTGGTGCAGATGCTCGACCGGCGGGAAAGTGTAATACTGACTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGcgcg                                                                                                            <  2:277436/140‑1 (MQ=255)
                             gATGCTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTc                                                                                                    <  1:571273/140‑1 (MQ=40)
                               tGCTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCAc                                                                                                  <  2:142124/140‑1 (MQ=40)
                                  tCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATCCAAAGCCATATGTACCCGGTATACATGCCGGCGCGAAAAATTCACCTg                                                                                               >  2:281995/1‑140 (MQ=255)
                                                aGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCa                                                                                 >  1:597567/1‑140 (MQ=40)
                                                           ggCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATGCACCTGTACCACTGCGACCATCGCGGCCTGc                                                                      >  2:319811/1‑140 (MQ=37)
                                                              tGACCGGGTGAGTGAGTAAAGCTGCCGCTGCGTTGAATCCTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGc                                                                   <  2:341443/140‑1 (MQ=14)
                                                              tGACCGGGTGAGTGAAGAAAGCAGCTGCTAGCTGGCACCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGc                                                                   <  1:298234/140‑1 (MQ=14)
                                                                        agtgagGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTAt                                                         <  2:554645/140‑1 (MQ=255)
                                                                          tgagGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAACTTCACCTGGACCGCAGCCACCATCGGGGCCTGCCGCTGGCCCTTATCa                                                       >  2:339891/1‑140 (MQ=14)
                                                                             ggAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCa                                                    <  1:319811/140‑1 (MQ=255)
                                                                             ggAAAGCCGCCGCTGGCTGGCATCGCGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCa                                                    <  1:289541/140‑1 (MQ=255)
                                                                             ggAAAGCCGCCGCTGGCAGGCATCGTGCGGCCTGATGGTGGCGCAGATTCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCa                                                    <  2:270566/140‑1 (MQ=255)
                                                                              gAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCAc                                                   >  1:709678/1‑140 (MQ=255)
                                                                                 aGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGa                                                <  2:709678/140‑1 (MQ=255)
                                                                                         ctggctggCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCCCCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGacaa                                        <  2:607903/140‑1 (MQ=255)
                                                                                         ctggctggCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGacaa                                        <  2:597567/140‑1 (MQ=255)
                                                                                                   tCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTa                              >  1:460266/1‑140 (MQ=255)
                                                                                                   tCGTGCGGCCTGACGGTGGAGCAGATGCAAAACCAGATGGACCCGGTGTACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTa                              <  1:580043/140‑1 (MQ=2)
                                                                                                    cGTGCGGCCTGACGGTGCCGCAGATGCAAAGCCAGATGGACCCGTTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTAc                             <  1:455316/140‑1 (MQ=255)
                                                                                                      tGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATGAGCGCGAAAGGGATAACAGCGTGGTACGc                           >  1:193551/1‑140 (MQ=255)
                                                                                                      tGCGGCCTGACGGTGGAGCAGATGCAAAACCAGATGGACCCGGTGTACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATGAGCGCGCAAGGGACAACAGCGTGGTAcac                           >  1:242903/1‑138 (MQ=11)
                                                                                                      tGCGGCCTGACGGTGGAGCAGATGCAAAACCAGATGGACCCGGTGTACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGc                           <  1:621846/140‑1 (MQ=255)
                                                                                                      tGCGGCCTGACGGTGGAGCAGATGCAAAACCAGATGGACCCGGTGTACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGc                           >  1:467168/1‑140 (MQ=255)
                                                                                                       gCGGCCTGACGGTGGTGCAGATACATAGCCAGATGGAGCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCa                          <  1:339891/140‑1 (MQ=255)
                                                                                                        cGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAg                         >  2:107463/1‑140 (MQ=255)
                                                                                                             tGACGGTGGAGCAGATGCAAAACCAGATGGACCCGGTGTACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATAc                    >  2:648547/1‑140 (MQ=11)
                                                                                                                cGGTGGCGCAGATGCGAAGCCACATGGACACGGTATATACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGAt                 <  1:284434/140‑1 (MQ=255)
                                                                                                                  gTGGAGCAGATGCAAAACCAGATGGACCCGGTGTACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGa               <  1:43300/140‑1 (MQ=255)
                                                                                                                     gcgcAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCCTATCAGCAAGGATGGGACAACAGCGCGGTAAGCAGAATACGATGAATg            >  2:284434/1‑140 (MQ=14)
                                                                                                                     gcgcAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCATATCAGCATGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATg            >  2:224596/1‑140 (MQ=255)
                                                                                                                     gagcAGATGCAAAACCAGATGGACCCGGTGTACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATg            >  2:700735/3‑140 (MQ=0)
                                                                                                                         aGATGCAAAGCCAGAGGGACCCCGTTTACACGCCGGCACGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGt        <  1:281995/140‑1 (MQ=255)
                                                                                                                             gCAAAACCAGATGGACCCGGTGTACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCGCGGAAGGGGCAAAAGCGTGGTACGCAGAATACGATGAATGGGGTAAcc    >  2:218397/1‑140 (MQ=11)
                                                                                                                              cAAAACCAGATGGACCCGGTGTACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACct   <  1:408014/140‑1 (MQ=255)
                                                                                                                               aaaaCCAGATGGACCCGGTGTAAACGCCGACGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACctg  <  1:285256/140‑1 (MQ=14)
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AGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACCTG  >  NC_000913/732844‑733110

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑