Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,560,985 C→A 21.2% intergenic (+87/‑383) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,560,9850CA21.2% 74.5 / 3.9 39intergenic (+87/‑383)yffL/yffMCPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base C (13/17);  new base A (5/4);  total (18/21)
Fisher's exact test for biased strand distribution p-value = 7.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAG  >  NC_000913/2560841‑2561129
                                                                                                                                                |                                                                                                                                                
ggCAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCaaa                                                                                                                                               <  1:431419/148‑1 (MQ=255)
     aaaGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTg                                                                                                                                          <  6:307190/148‑1 (MQ=255)
              gCACCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAg                                                                                                                                  <  1:132491/147‑1 (MQ=255)
               cAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAgg                                                                                                                                 <  6:383389/147‑1 (MQ=255)
                aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCaaaa                                                                                                                                              <  8:340715/133‑1 (MQ=255)
                aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCaaaa                                                                                                                                              >  7:340715/1‑133 (MQ=255)
                     aTACCAGTTATTATTCAAGCCGTACAACCTGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCa                                                                                                                          <  6:401101/148‑1 (MQ=255)
                     aTACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCATAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCa                                                                                                                          <  7:103756/148‑1 (MQ=255)
                          aGTTATTATTAAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCTCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTTGGTAAAAATTTGCCTTTAATGTGGGAAAAAAg                                                                                                                      >  1:420264/1‑147 (MQ=255)
                           gTTATTATTCAAGCCGTACAACATGAAATAACGTAATCAGGCGGGCAATGTTCACGCCTTTTATTTGCCTTAAATCCATGAATTCAGGGGTGTCAAAAGTTGCCCTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGtt                                                                                                                    <  6:369065/148‑1 (MQ=255)
                           gTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTGATTGGTGTGTAAAAAGTAGACTTTAAGGAGTGTCAAAAttt                                                                                                                    >  8:257345/1‑148 (MQ=255)
                            ttattaTTCTAGCAGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGGCTTTTCTTTGCCTTAATTCCATGATTTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTg                                                                                                                   <  8:183829/148‑1 (MQ=255)
                             tattatTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATTGTTGGGTAAAATTTTGCCTTAAAGGTGGGGAAAATGTTg                                                                                                                   >  7:325925/1‑147 (MQ=255)
                             tattatTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTg                                                                                                                               >  6:124630/1‑135 (MQ=255)
                             tattatTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTg                                                                                                                               <  5:124630/135‑1 (MQ=255)
                             tattatTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTGAATGATGGGTAAAAAGTTTCCTTTAAGGAGCGTGAAAAGttt                                                                                                                   >  2:373983/1‑146 (MQ=255)
                             tattatTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCAGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGTTTGGTAAAAATTTGACTTTAAGGAGGGTCAAAATTTg                                                                                                                   >  4:402752/1‑147 (MQ=255)
                                  ttCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATTGGTGGGTCAAAAGTTGCAGTTAAGGTGGGTCAAAATTTGCAGtt                                                                                                              >  5:310705/1‑147 (MQ=255)
                                  ttCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAATGTTGCCGTTTAGGGGGGTGGAAATTTggagtg                                                                                                              >  5:52801/1‑142 (MQ=255)
                                       gacGTATAACATGAAATAACGGAATAAGCAGTGCAATTTTCCCTCCTTTTCTTTGCCTTAATTCAATGAATTCATGTGGGTCATAAGTTGCCGTTTTTGTTGGGTAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAgg                                                                                                          <  6:301744/144‑1 (MQ=25)
                                                                cAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAg                                                                                                                                  >  7:211545/1‑97 (MQ=255)
                                                                cAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAg                                                                                                                                  <  8:211545/97‑1 (MQ=255)
                                                                  ggCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTGAGTGGTGGGTCAAAATATGCATTTTAGGAGGGTGAAATTTTGGCGTATAGGTGTGTGAAATTTTGACTAGTAAGGAttg                                                                              >  3:166921/1‑146 (MQ=255)
                                                                            gTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGATAATGGTGGCTCAAAAGTTGCCGTTAAGGAGGGTCAAAAGTTGCCGTTAAGGTGGCTGAAAAGTTGACTCGTAAGCATTGTACTAGTAAg                                                                    >  3:202930/1‑147 (MQ=25)
                                                                                                ttAATTCCATGAATTCAGGTGGGTCTAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTaa                                                                                                                                   <  3:143536/64‑1 (MQ=255)
                                                                                                                  tctgctaaaaaGTACCCCTTATTGCTGGGTAAAAACCTGCCTTTAAGGTGGGTCAAAAGGTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCcggtcg                               <  7:257345/139‑1 (MQ=37)
                                                                                                                       ttctaatttGCCTTTATTGTGGGGTAAATACTAGCAGTTCAGTTGGTTCAAACTATGCCGTTCAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATag                        <  2:338026/141‑1 (MQ=255)
                                                                                                                         aaaaGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTTAGGTGGGTCAAAAGTTGCAGTTAAGGTGGGGCTAATGTTGACGAGAAAGAATTCTACTATTAAGATTTCTAGGCGACGGGAGTTTTTTAGCCTATCGGTCGGTCATa                         >  1:171361/1‑145 (MQ=37)
                                                                                                                          aaaGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTTAGGTGGGTCAAAAGTTGCCGAGTAAGATGTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTATCCTCCCGGTCGGTCATagagc                     >  2:295143/1‑147 (MQ=255)
                                                                                                                                   gTTTGTGGGGGGTCAAATGTTGCCTTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTag            <  5:334358/148‑1 (MQ=255)
                                                                                                                                   gTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGcc               >  3:36148/1‑145 (MQ=255)
                                                                                                                                   cttAGTGGTTCGTCAAAAGATTCCGTTAAGGTTGGTCAAAATTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTag            <  3:164288/147‑1 (MQ=38)
                                                                                                                                     tAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGtttt                                              <  2:339696/112‑1 (MQ=255)
                                                                                                                                     tAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGtttt                                              >  1:339696/1‑112 (MQ=255)
                                                                                                                                      aGTGCTGGGTCATTACTAGCCTTTTAGGTGGGTTAAATGTTGCCTTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTagag          <  8:236412/147‑1 (MQ=255)
                                                                                                                                       ctggtggGTCAATACGAGCCGTTTAGTTGGGTAAAATGTAGCCGTTCAGGTGGGTCAAAAGTTGCCGAGTACGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGGCGCCTAGAGt         <  5:28743/146‑1 (MQ=255)
                                                                                                                                         ggtggGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAATGTGGGACAAAAGTTTCAGAGAAAGAATTCTACAATTAAGAATTCAAGGCGACGGCAGTTATTTATCATCACGGGCGGTCATAGAGAGGCGAATAGAGTTa       >  4:186447/1‑147 (MQ=21)
                                                                                                                                           tggGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTaaa     >  7:138059/1‑147 (MQ=255)
                                                                                                                                            gggTAAATAGTTGCCGTTTAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACa   <  6:310705/148‑1 (MQ=255)
                                                                                                                                                cAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACag  >  7:113842/1‑145 (MQ=255)
                                                                                                                                                cAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACag  >  1:84125/1‑145 (MQ=255)
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GGCAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAG  >  NC_000913/2560841‑2561129

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑