Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,560,996 G→T 27.0% intergenic (+98/‑372) 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_0009132,560,9960GT27.0% 63.6 / 5.7 41intergenic (+98/‑372)yffL/yffMCPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (16/13);  new base T (4/7);  total (21/20)
Fisher's exact test for biased strand distribution p-value = 4.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATT  >  NC_000913/2560854‑2561139
                                                                                                                                              |                                                                                                                                                
tGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAgg                                                                                                                                            <  5:18797/149‑1 (MQ=255)
  cAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTAAAGGtt                                                                                                                                          >  3:354018/1‑148 (MQ=255)
   aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGGTAAGGTgg                                                                                                                                        >  3:313098/1‑149 (MQ=255)
     cGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGt                                                                                                                                      <  7:396002/149‑1 (MQ=255)
         tACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTGAAGTGGGGTCaa                                                                                                                                   >  1:162286/1‑148 (MQ=255)
            cAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTGTGTGGGGGGTCAAAAGTTGCCGTTTAGGGGTGTCAAAAGt                                                                                                                               >  3:314494/1‑149 (MQ=255)
            cAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGATTATGTTTGGTAAAAATATGAATTTAAGGAGGGGCaaattt                                                                                                                               >  8:288080/1‑146 (MQ=255)
             aGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTTTTGTTGGGTCATATTTTGACTTTAAGGAGGGTGAAAAg                                                                                                                                >  1:348902/1‑147 (MQ=255)
                tattttTCAAGCCGTACAACATGAAATAACGTTATCAGGCGTGCAATTTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGGTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGc                                                                                                                            <  4:257493/148‑1 (MQ=255)
                    attCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGAGACTGGTGGGTAAAATGATGCATTGAAGGAGTGTCAAAAGTTgaagta                                                                                                                        >  4:219407/1‑143 (MQ=255)
                     ttCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTaa                                                                                                                      <  6:326176/149‑1 (MQ=255)
                      tCAATCCGTAAAACATGAAATATCGTAATCAGTCGTGCAATGATCCCGCCTTTTCTTGTCCTTAATTAAATGTATTCTGGTGGTTAAATAGAAGCCGTTTTTGGTGGGTAAAATGTAGGAGTTAAGGTGGGTCAAAAGTTGCCGTTAAg                                                                                                                     <  2:162286/149‑1 (MQ=255)
                      tCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGTGTCAAAAGTTGCCTTTAAGGTGGGTAAAAAGTTGCAGTGaac                                                                                                                     >  7:384409/1‑148 (MQ=255)
                                      gAAATAACGGAATCAGGCGGGCAATTTTCCGGCCTTTTGTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAATTTGCCGTTAAGGTGGGTCAAAAGTTGcc                                                                                                                           <  5:263574/127‑1 (MQ=255)
                                       aaaTAACGGAATCAGTAGGCCATTTTTCCCGCCTTTTGTTTGCCTTAAATCCATGAATTCAGGCGGGTCAAAAGTTGCCGTTATTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGc                                                                                                     <  1:115388/148‑1 (MQ=25)
                                           aaCGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCTTTAAGGTGGGTCAAAAGtt                                                                                                                              <  2:138427/119‑1 (MQ=255)
                                           aaCGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCATTAAGGTGGGTCAAAAGtt                                                                                                                              >  1:138427/1‑119 (MQ=255)
                                            aCGGAATCAGCCGCGCAATGTTCCCGCCTTTGCTTTTCCTTAAATCCATGAATTCAGGTGGGTGAAAAGTTTCCGTTAGTGGTGGGTCAAATGTTGCCTTTACTGTGGGTCAAAAGTTGCCCTTAAGGTGGGTCAAAAGTTGCCGAGt                                                                                                <  5:101085/148‑1 (MQ=37)
                                                                   ccGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGATCAAAAGTTGCCGTTAAGGTGTGGCAAAATTTGAAGAGAAAGAATTCTACTATTAAGAAtta                                                                         >  1:375312/1‑147 (MQ=37)
                                                                     gCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGGGGGTCAAAAGTTGCCGTTAAGGTGGGGCAAAAGTTGCCTAGTAAGCAGTCGACTATTTAGAATTCTAg                                                                      >  7:322375/1‑149 (MQ=37)
                                                                        ttttCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGTTGGGTAAAAAGTTGCCGTAAAGGTGGGTCAAAATTTTGAGTTAAGGTGGATGAAAAGTTGCCGAGAAAGAATTCTACAATTAAGAATTCAAGGc                                                                    >  6:220056/1‑148 (MQ=37)
                                                                                                        cgTCAAAATTTCCCTTTAGTGGGTGGACTTAAGTCGCGTTAAATTCGGTTCAAAAGTTTCCCTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATa                                   <  5:296770/148‑1 (MQ=255)
                                                                                                          taaaaaGATGGCCTTAGTGGTGGGTAACAACCTGCCGTTAATTTGGGTCAAAAGTAGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATaga                                 <  7:288080/147‑1 (MQ=37)
                                                                                                          tCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGAAGTTAAGGTGGGTCAAAATTTTCAGAGTAAGAATTCTACAATTAAGAATTCTAGGAGTCGTGAATTTTTTATAATACCTGTCGGTCATa                                   >  2:360377/1‑147 (MQ=21)
                                                                                                            aaaaTTTGCCGTTACTGGGGGGTCAAAAGGTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATagaga                               <  3:219407/149‑1 (MQ=255)
                                                                                                                  tcccGTTTATGGTGGGTCAAAACCTGCCTTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGcc                         <  4:314494/147‑1 (MQ=38)
                                                                                                                    ccGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGcc                         >  1:163392/1‑147 (MQ=255)
                                                                                                                     cGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGcc                         >  7:212039/1‑146 (MQ=255)
                                                                                                                     acttcgtggtgGGTCAAATGTTGCCTTTAAGGTGGGTCAAAAGTTTCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTa                       <  8:322375/143‑1 (MQ=255)
                                                                                                                            gttttgTCATATGTTGCCTTTTAGTTGGGTCAAATGTTGCCTTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTaaa               <  2:375312/144‑1 (MQ=255)
                                                                                                                             gtggGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTaaa               >  8:265496/1‑148 (MQ=255)
                                                                                                                             gtggGTAAAATGTTGCCGTTACTGTGGGTCAAAAGTTTCCGTTCAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTaaa               <  1:70001/148‑1 (MQ=38)
                                                                                                                               gggTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTaaa               >  8:217890/1‑146 (MQ=255)
                                                                                                                                 gTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACag            >  4:283117/1‑147 (MQ=255)
                                                                                                                                 ctCAAACGTTGCCTTTAAGTTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACagaa          <  5:220056/148‑1 (MQ=255)
                                                                                                                                  tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTATGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACag            >  6:76169/1‑146 (MQ=255)
                                                                                                                                    aaatGTCGCCTTTAATGTGGGTCAATAGTATCATTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAgaagaa       <  7:6452/149‑1 (MQ=255)
                                                                                                                                    aaaaGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGtt                  <  7:217011/138‑1 (MQ=255)
                                                                                                                                    aaaaGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGtt                  >  8:217011/1‑138 (MQ=255)
                                                                                                                                    aaaaGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTATACAATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGGCGGTCATAGAGAGTCGCCTAGAGTTAAACAgaagaa       >  3:54472/1‑149 (MQ=255)
                                                                                                                                     aaaGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAat      <  5:76169/149‑1 (MQ=255)
                                                                                                                                              gTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAattatt  <  6:367923/144‑1 (MQ=255)
                                                                                                                                              gTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAattatt  >  5:367923/1‑144 (MQ=255)
                                                                                                                                              |                                                                                                                                                
TGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATT  >  NC_000913/2560854‑2561139

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: