Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,560,996 G→T 13.9% 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_0009132,560,9960GT13.9% 95.8 / 4.2 47intergenic (+98/‑372)yffL/yffMCPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (20/19);  new base T (3/4);  total (23/24)
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

AACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTAT  >  NC_000913/2560857‑2561138
                                                                                                                                           |                                                                                                                                              
aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAgcggg                                                                                                                                       >  1:154960/1‑145 (MQ=255)
aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTgg                                                                                                                                       <  3:298021/149‑1 (MQ=255)
aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTgg                                                                                                                                       <  2:89510/149‑1 (MQ=255)
 aCGAATACCAGTTATTATTCAAGCCGTACCACATGAAATAACCGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTggg                                                                                                                                      <  6:376065/149‑1 (MQ=255)
 aCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTggg                                                                                                                                      <  3:368703/149‑1 (MQ=255)
        ccAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATAGGTGTGTAAAAAGTAGCATTGAAGGAGGGTCaaaat                                                                                                                               >  8:426960/1‑148 (MQ=255)
         cAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAAAGGTGGGTAAAAAGATGCCGTTAAGGAGGGTCaaaatt                                                                                                                              >  3:154014/1‑147 (MQ=255)
          aGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGtt                                                                                                                             <  8:420232/149‑1 (MQ=255)
           ggaattattCAACCCCTACATCATGAAATAACCGAATCAGGCGCGCAATCTTGCCGCCTTTTCTTTGCCATAATTCCATGCATTCAGGTGGGCAAAATGTTGCCGTTAGCGGTGGGTCAAATGTTGCCGTTAAGGTGGGTCAAAAGTTg                                                                                                                            <  6:66293/146‑1 (MQ=25)
           gTTATTATTCTACCAGTATAACATGAAATAAAGGTATCTGGCTTGCATTTATCCAGGCTTTTGTTTGGCTTAATTACATGAATTCTTGTTGGTTAAAAGTTCGCGTTATTGGTGGTTATAAAGTTTCCGTTAAGGTGGGTCAAAAGtt                                                                                                                             <  6:168566/148‑1 (MQ=255)
           gTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTc                                                                                                                                    <  8:328893/141‑1 (MQ=255)
           gTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTc                                                                                                                                    >  7:328893/1‑141 (MQ=255)
              attattCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTACCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCg                                                                                                                         >  1:349118/1‑149 (MQ=255)
                tattCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAATTTgactt                                                                                                                        >  7:45012/1‑144 (MQ=255)
                 attCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAg                                                                                                                                           >  2:18920/1‑128 (MQ=255)
                 attCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAg                                                                                                                                           <  1:18920/128‑1 (MQ=255)
                 attCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGAGAGTGGTGTGTAAAAATTTGCCGTCTAGGGGGCGCAAAATTTgaagtg                                                                                                                       >  8:379400/1‑143 (MQ=255)
                 actCACGCCGTACTACATGCAATAAAGCAATCAGTCGTCCAATGTTACCGCCTTTTCTTTGCCTTTATTGCATGTATTCAGGGGGGGCAAAAGTTGCCGTTAGTTGTGGGTCAAAAGTTGCCCTTAAGGTGGGTCAAAAGTTGCCGtt                                                                                                                       <  2:154960/146‑1 (MQ=21)
                  ttCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGTTGGGTAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGccttgag                                                                                                                     >  7:46955/1‑144 (MQ=255)
                   tccaGCCGTACCACATGAAATACAGGACTCTCGACGGCACTTTTTACTCCTTTTCTTTGCCTTTAATCCATGCATTCAGGCGGGTCAACTGCCGCCCTTTTTTGTGGCTCAAAACATTCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAg                                                                                                                    <  2:349118/146‑1 (MQ=255)
                   tCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATTGGTGGGTCAAAAGTTGCCTTTAAGGGGGGTCAATAGTTGAAGTTAAg                                                                                                                    >  1:223787/1‑149 (MQ=255)
                              cacaTGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGTGTAAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCaaaa                                                                                                         <  5:100720/148‑1 (MQ=255)
                                     aaTAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGGTAAGGGGGGTGTAAATTTGACg                                                                                                  >  7:277714/1‑149 (MQ=38)
                                         ccGGAATCAGGCGGGCCATGATCCCGCATTTTCGATGCCTTAATTCCAAGAATTCAGGCGGGTAAAAAGCGCCCGTTAGAGGTGGGTCAAAACCTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTa                                                                                                                      <  1:419712/124‑1 (MQ=21)
                                                        cAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATTGGTGGGTCAAAAGTTGACGTTAAGGTGTGTGAAAAGTTGCCGTTTATGTGGGTCAAAAGTTGCAGAGTAAGAATTCTACAAtaa                                                                               >  1:118082/1‑147 (MQ=37)
                                                           tGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATTGGTGGGTAAAAAGTTGCAGTTAAGGTGGCTCAAAATTTGAATTTAAGGTGTGTCAAAATTTGACTAGTAAGAATTATAATATTAAg                                                                             >  3:218795/1‑148 (MQ=25)
                                                           tGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCTTTAAGGTGGGTCAATTTTTGCAGTTAAGGGGGGTCAAAATTTTACTAGAAAGAATTGTACAAtatag                                                                             >  3:7856/1‑144 (MQ=25)
                                                                             gCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGGCAAAAGTTGGAGTTAAGGTGGGGGAAAAGTTGACTAGAAAGCATTCTAATATAATGAATACTAGGCGACGGGAGt                                                          >  5:324163/1‑149 (MQ=25)
                                                                              ccTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTGATGGTGGGTGAAAAGTTGCCGTTAAGGTGGGTCAATAGTTGCCGAGTAAGAATTCTTCTATTAAGATTTCTAGGCGGCGGGAGtt                                                         >  7:181409/1‑149 (MQ=37)
                                                                                  aaTTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAATTTGCAGTTTAGGTGGCTCAAAAGTTGCGGAGTAAGAATTCTACAATAAAGAATTGTACGCGTCGGGAGtgtttt                                                     >  7:346706/1‑149 (MQ=25)
                                                                                  aaTTCCATGAATTCAGGGGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGGCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGttttt                                                      <  1:109746/148‑1 (MQ=255)
                                                                                   aTTTCATGAATTCCGGTGTGTTAAAATATGCCCTTATTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGtttttt                                                     <  8:45012/148‑1 (MQ=25)
                                                                                       cATGAATTCAGGTGGGTCAAAAGTTGCCGTTAATGTTTGGTCAAAAGTTGCAGTTAAGGTGGGTCAACATTTGGCGATAACGTGGCGCAAAAGTTGACGAGAAAGAATTATAAAATTAAAATTTAAAGGCGACGGGAGTGTTTTaaact                                                >  2:316714/1‑145 (MQ=16)
                                                                                                ctgTGGGTCAAAAGAAGCCGTTCTGGGGGGGTAAAAACACGCCTTTAAGGTGGGTAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCcggtcgg                                       <  7:273373/147‑1 (MQ=37)
                                                                                                   tGGGTCAAAAGCAGGCGTTAGGGGTGGGTCAAAACGAGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCa                                    <  7:426960/149‑1 (MQ=38)
                                                                                                      gTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGACAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCAGGTCGGTCa                                    >  3:153695/1‑146 (MQ=255)
                                                                                                          aaaGTTGGCTTTATTGGGGGGTCAATTCATGCCTTTTAGTTGGGTCAAAAGTTTGATTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATagaga                              <  8:258593/148‑1 (MQ=255)
                                                                                                           aatttGCCGTTAGTGGGGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTTCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGt                            <  3:88391/146‑1 (MQ=255)
                                                                                                                 cccttAGGGGTGGCTCAAATGCCGCCGTTAAGGTGGGGCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCTTAGAGAGTCGCCTa                      <  7:298288/146‑1 (MQ=38)
                                                                                                                   attAGTGGGGGGTAAATTGGTGCCTTTTAGTTGGGTTAAATGTTGCCGTTCAGGTGTGTCAAAAGTTTCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTaga                    <  2:222445/148‑1 (MQ=255)
                                                                                                                       gtggtgGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGCGTCGCCTAGCGtt                 >  6:264202/1‑148 (MQ=255)
                                                                                                                        tggtggGTCAAAAGTTGCCGTTAAGGTGGGTCAATAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCTACGGGAATTTTTTAGCATCCAGGTAGGTCATAGAGAGTCGCCTAGACTTa                >  6:269266/1‑148 (MQ=37)
                                                                                                                               tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAATAATTCTAGGAGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTAAAACag           >  5:113173/1‑146 (MQ=255)
                                                                                                                               tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGa                                                            <  3:350571/97‑1 (MQ=255)
                                                                                                                               tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGa                                                            >  4:350571/1‑97 (MQ=255)
                                                                                                                                 aaaacgtGCCGTTAAGGTGGGTGAAAAGTTGCAGTTAAGGTGGGTCAAAAGTTTCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAgaagaa      <  7:79947/143‑1 (MQ=255)
                                                                                                                                     gTTGACTTTAAGTTGTGTTAAATTTTTCAGTTAAGTTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAattat  <  2:237668/149‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                              
AACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTAT  >  NC_000913/2560857‑2561138

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: