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

TGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATT  >  NC_000913/2560854‑2561139
                                                                                                                                              |                                                                                                                                                
tGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAgg                                                                                                                                            <  5:18797/149‑1 (MQ=255)
  cAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTAAAGGtt                                                                                                                                          >  3:354018/1‑148 (MQ=255)
   aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGGTAAGGT‑gg                                                                                                                                        >  3:313098/1‑149 (MQ=255)
     cGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGT‑GGGt                                                                                                                                      <  7:396002/149‑1 (MQ=255)
         tACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTGAAGTG‑GGGTCaa                                                                                                                                   >  1:162286/1‑148 (MQ=255)
            cAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTGTGTGGGGGGTCAAAAGTTGCCGTTTAGGG‑GTGTCAAAAGt                                                                                                                               >  3:314494/1‑149 (MQ=255)
            cAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGATTATGTTTGGTAAAAATATGAATTTAAGGA‑GGGGCaaattt                                                                                                                               >  8:288080/1‑146 (MQ=255)
             aGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTTTTGTTGGGTCATATTTTGACTTTAAGGA‑GGGTGAAAAg                                                                                                                                >  1:348902/1‑147 (MQ=255)
                tattttTCAAGCCGTACAACATGAAATAACGTTATCAGGCGTGCAATTTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGGTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGT‑GGGTCAAAAGTTGc                                                                                                                            <  4:257493/148‑1 (MQ=255)
                    attCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGAGACTGGTGGGTAAAATGATGCATTGAAGGA‑GTGTCAAAAGTTgaagta                                                                                                                        >  4:219407/1‑143 (MQ=255)
                     ttCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTaa                                                                                                                      <  6:326176/149‑1 (MQ=255)
                      tCAATCCGTAAAACATGAAATATCGTAATCAGTCGTGCAATGATCCCGCCTTTTCTTGTCCTTAATTAAATGTATTCTGGTGGTTAAATAGAAGCCGTTTTTGGTGGGTAAAATGTAGGAGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAg                                                                                                                     <  2:162286/149‑1 (MQ=255)
                      tCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGTGTCAAAAGTTGCCTTTAAGGT‑GGGTAAAAAGTTGCAGTGaac                                                                                                                     >  7:384409/1‑148 (MQ=255)
                                      gAAATAACGGAATCAGGCGGGCAATTTTCCGGCCTTTTGTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAATTTGCCGTTAAGGT‑GGGTCAAAAGTTGcc                                                                                                                           <  5:263574/127‑1 (MQ=255)
                                       aaaTAACGGAATCAGTAGGCCATTTTTCCCGCCTTTTGTTTGCCTTAAATCCATGAATTCAGGCGGGTCAAAAGTTGCCGTTATTGGTGGGTCAAAAGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGc                                                                                                     <  1:115388/148‑1 (MQ=25)
                                           aaCGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCTTTAAGGT‑GGGTCAAAAGtt                                                                                                                              <  2:138427/119‑1 (MQ=255)
                                           aaCGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCATTAAGGT‑GGGTCAAAAGtt                                                                                                                              >  1:138427/1‑119 (MQ=255)
                                            aCGGAATCAGCCGCGCAATGTTCCCGCCTTTGCTTTTCCTTAAATCCATGAATTCAGGTGGGTGAAAAGTTTCCGTTAGTGGTGGGTCAAATGTTGCCTTTACTGT‑GGGTCAAAAGTTGCCCTTAAGGTGGGTCAAAAGTTGCCGAGt                                                                                                <  5:101085/148‑1 (MQ=37)
                                                                   ccGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGT‑GGATCAAAAGTTGCCGTTAAGGTGTGGCAAAATTTGAAGAGAAAGAATTCTACTATTAAGAAtta                                                                         >  1:375312/1‑147 (MQ=37)
                                                                     gCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGG‑GGGTCAAAAGTTGCCGTTAAGGTGGGGCAAAAGTTGCCTAGTAAGCAGTCGACTATTTAGAATTCTAg                                                                      >  7:322375/1‑149 (MQ=37)
                                                                        ttttCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGTTGGGTAAAAAGTTGCCGTAAAGGT‑GGGTCAAAATTTTGAGTTAAGGTGGATGAAAAGTTGCCGAGAAAGAATTCTACAATTAAGAATTCAAGGc                                                                    >  6:220056/1‑148 (MQ=37)
                                                                                                        cgTCAAAATTTCCCTTTAGTGGGTGGACTTAAGTCG‑CGTTAAATTCGGTTCAAAAGTTTCCCTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATa                                   <  5:296770/148‑1 (MQ=255)
                                                                                                          taaaaaGATGGCCTTAGTGGTGGGTAACAACCTGCCGTTAATTT‑GGGTCAAAAGTAGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATaga                                 <  7:288080/147‑1 (MQ=37)
                                                                                                          tCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGT‑GGGTCAAAAGTTGAAGTTAAGGTGGGTCAAAATTTTCAGAGTAAGAATTCTACAATTAAGAATTCTAGGAGTCGTGAATTTTTTATAATACCTGTCGGTCATa                                   >  2:360377/1‑147 (MQ=21)
                                                                                                            aaaaTTTGCCGTTACTGGGGGGTCAAAAGGTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATagaga                               <  3:219407/149‑1 (MQ=255)
                                                                                                                  tcccGTTTATGGTGGGTCAAAACCTGCCTTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGcc                         <  4:314494/147‑1 (MQ=38)
                                                                                                                    ccGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGcc                         >  1:163392/1‑147 (MQ=255)
                                                                                                                     cGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGcc                         >  7:212039/1‑146 (MQ=255)
                                                                                                                     acttcgtggtgGGTCAAATGTTGCCTTTAAGGT‑GGGTCAAAAGTTTCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTa                       <  8:322375/143‑1 (MQ=255)
                                                                                                                            gttttgTCATATGTTGCCTTTTAGTT‑GGGTCAAATGTTGCCTTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTaaa               <  2:375312/144‑1 (MQ=255)
                                                                                                                             gtggGTCAAAAGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTaaa               >  8:265496/1‑148 (MQ=255)
                                                                                                                             gtggGTAAAATGTTGCCGTTACTGT‑GGGTCAAAAGTTTCCGTTCAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTaaa               <  1:70001/148‑1 (MQ=38)
                                                                                                                               gggTCAAAAGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTaaa               >  8:217890/1‑146 (MQ=255)
                                                                                                                                 gTCAAAAGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACag            >  4:283117/1‑147 (MQ=255)
                                                                                                                                 ctCAAACGTTGCCTTTAAGTT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACagaa          <  5:220056/148‑1 (MQ=255)
                                                                                                                                  tCAAAAGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTATGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACag            >  6:76169/1‑146 (MQ=255)
                                                                                                                                    aaatGTCGCCTTTAATGT‑GGGTCAATAGTATCATTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAgaagaa       <  7:6452/149‑1 (MQ=255)
                                                                                                                                    aaaaGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGtt                  <  7:217011/138‑1 (MQ=255)
                                                                                                                                    aaaaGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGtt                  >  8:217011/1‑138 (MQ=255)
                                                                                                                                    aaaaGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTATACAATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGGCGGTCATAGAGAGTCGCCTAGAGTTAAACAgaagaa       >  3:54472/1‑149 (MQ=255)
                                                                                                                                     aaaGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAat      <  5:76169/149‑1 (MQ=255)
                                                                                                                                              gTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAattatt  <  6:367923/144‑1 (MQ=255)
                                                                                                                                              gTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAattatt  >  5:367923/1‑144 (MQ=255)
                                                                                                                                              |                                                                                                                                                
TGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGT‑GGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATT  >  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: ‑