Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,560,985 C→A 20.8% 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_0009132,560,9850CA20.8% 64.5 / 2.7 40intergenic (+87/‑383)yffL/yffMCPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base C (16/15);  new base A (4/5);  total (20/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAG  >  NC_000913/2560843‑2561129
                                                                                                                                              |                                                                                                                                                
cAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGATTTCAGGTGGGTCAAAAGTTGCCTTTAGTGGTGGGTCaaaa                                                                                                                                              <  1:334400/147‑1 (MQ=255)
cAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGt                                                                                                                                            <  5:300054/149‑1 (MQ=255)
   aaaGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGTGTCAAAAGttcc                                                                                                                                         >  3:272728/1‑147 (MQ=255)
             cAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGt                                                                                                                                <  6:89449/148‑1 (MQ=255)
             cAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGt                                                                                                                                <  7:79903/148‑1 (MQ=255)
             cAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGGGGTGGGTCAAAAGTTGCCGTTAAGGt                                                                                                                                <  1:60751/148‑1 (MQ=255)
             cAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTATTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGTTGGGTAAAAGTTTGCAGTGAAgagg                                                                                                                               >  5:378798/1‑146 (MQ=255)
             cAACGAATACCAGTTATTATTCAAGCCGTACAACAAGAAATAACGGAATCAGGCGGGCAATGTTCCCTCCTTTTCTTAGCCTTAATTCAATGAATTCAGGTGGGTCAAAAGTTGCCGTTACTGCTGAGTCAAAATTATCCGTTAAggag                                                                                                                               >  1:269725/1‑147 (MQ=255)
              aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTgg                                                                                                                              >  6:57423/1‑149 (MQ=255)
              aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTgg                                                                                                                              <  4:211614/149‑1 (MQ=255)
              aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTgg                                                                                                                              <  2:369863/149‑1 (MQ=255)
                     aCCAGTTATTACTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGGCAAAAGTTGCCGTTAAGGTGGGTCaaaa                                                                                                                       <  7:418478/149‑1 (MQ=255)
                      ccAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGGCAAAAGTTGCCGTTAAGGTGGGTCaaaa                                                                                                                       <  6:270838/148‑1 (MQ=255)
                      ccAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGATAGTGGTGGGTCAAAAGTTGCCGGTAATGTGGGTCAAAAg                                                                                                                      >  3:181741/1‑149 (MQ=255)
                       cAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGTTGTTTAAAAAGTTGCATTTAAGGTTGGTCAAATGt                                                                                                                     >  5:293622/1‑149 (MQ=255)
                       cAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGTTGGGTCAAACGTTGCCGTTAAGGTGGGTCAAAAGt                                                                                                                     >  1:245492/1‑149 (MQ=255)
                       cAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGACTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGATAGTGGTGGGTCAAATTTTGACGTTTAGGTGGGTCAAAAGt                                                                                                                     >  1:333951/1‑149 (MQ=255)
                         gTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTTTAGGTGGCTAAAAATTTGACTTTAAGGATTGACAAAAGtag                                                                                                                   >  3:341648/1‑147 (MQ=255)
                         gTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTGAGTGGTGGGGAAAAAGTTGACGTTAAGGAGTGTCAAAAttt                                                                                                                    >  8:180291/1‑148 (MQ=255)
                            aatattCAATCCGTTCAACAAGAAATATCTGAATCATGCTTGCATTGTTTCCTCATTTTCTTTTCCTTTATTCAATGTATTCAGGTGGGTAATAAGTTCGCGTTTGTTGTGGGTCAAAAGTTTGATTTAAGGTGGGTCAAAAGTTGcc                                                                                                                 <  4:181741/146‑1 (MQ=255)
                             ttattCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCATAATATGACTTTAAGGTGGGTCAAAAGTTGCAGt                                                                                                               >  5:149998/1‑149 (MQ=255)
                                     gCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTgg                                                                                                       <  5:57423/149‑1 (MQ=255)
                                            aacaTGAAATAACGTAATAAGCCCTGCATTCTTCCCGGCTTTTCTTTTCCTTAATTACATGAATTCAGGTGGGTAAAAAGTTGCCGTTATTGGTGGGTAAAATGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCaaaa                                                                                                <  2:351097/149‑1 (MQ=25)
                                                  aaaTAATGGAATATGTCTGGCATTTTTCCCGCCGTTTCTATTCCTTAAATACATGAATTCAGGTTTCTCAAAAGTTGCCTTTACTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTAAAAAGTTGCCTTTAAGGTGGGTCAAAAGTTGc                                                                                           <  8:375800/148‑1 (MQ=16)
                                                                       acttatCCAGCCCTTCCTTTGCCATAATTTCATGAATGCCGCGGGGCATAAATCAGCCATTACGGGGGGCTAACTAGCTGCCTTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTaa                                                                     <  2:293739/144‑1 (MQ=12)
                                                                         tGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGTGTCAAAAGTTGAAGTTAAGGTGTGTGACATTTTGAAGAGTAAGGAGTGTACTATTatt                                                                    >  5:350323/1‑146 (MQ=21)
                                                                                   ttttCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGAGAGTAAAAATTTGCAGTTAAGGTGGGGCAAAAGTTGACTAGAATTAAGACTAAGAATAAGAATACTAGGc                                                          >  5:229757/1‑148 (MQ=21)
                                                                                                  atacATGAATTCCGCTGGGCCAAAAGAAGGCCTTCTGGGGGGGTAAAAACCTGCCGTTAAGGTGGCTCAAAAGTTGCCCTTCAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTa                                           <  1:228849/145‑1 (MQ=255)
                                                                                                   tcaaTGAATTCATCTGGGTAAAAATTAGCCCTTAGTGGTGGCTAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGc                                         <  7:180291/146‑1 (MQ=37)
                                                                                                                     tCAACAGTGGCCGTTCGTTCTGCTTAAAACGTTGCCTTTATGGGGGGTCAAAAGTTGCCGTAAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATaga                       <  3:238592/149‑1 (MQ=37)
                                                                                                                        aaaGTTGCCGTTAGTGGTGGGTCAAAAGTTGCGGTGAAAGAGGGGCAATATTTGGAGATATCGGGGGAGTAAATTATAGGAGTAAGGATTGTACGATTAAGAATTGTAGGGAGCGTGAGTTTTGTAGGCTATCGGAGGGTCATagaacg                    >  6:391496/1‑146 (MQ=255)
                                                                                                                                 gTTAGTGGTGGGTCAAAAGATGTCGTTACTGTGAGTAAAATGTTTCCTTTAAGGTGGGTCAAAAGTTGCCGAGTATGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTaga           <  6:229757/149‑1 (MQ=38)
                                                                                                                                       ggtggGTCAAAAGCTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTCAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTaaa     <  7:165456/149‑1 (MQ=255)
                                                                                                                                        tttggTCAAAAGTTTCCGTTAAGGTTGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTaga           <  4:1561/139‑1 (MQ=255)
                                                                                                                                        gtggGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTGAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTATAAGCCTCCCGGTCGGTCATAGATAGTCGCGTAGAGTTaac     >  6:15946/1‑147 (MQ=37)
                                                                                                                                        gtggGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTaga           >  3:1561/1‑142 (MQ=255)
                                                                                                                                            gTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACag  >  3:92950/1‑147 (MQ=255)
                                                                                                                                             tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACag  >  5:314377/1‑146 (MQ=255)
                                                                                                                                             tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACag  >  1:165891/1‑146 (MQ=255)
                                                                                                                                             tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACag  >  7:402735/1‑146 (MQ=255)
                                                                                                                                              |                                                                                                                                                
CAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAG  >  NC_000913/2560843‑2561129

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: ‑