Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,560,985 C→A 31.8% intergenic (+87/‑383) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein YffL/CPZ‑55 prophage; uncharacterized protein YffM

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,560,9850CA31.8% 45.9 / 5.9 35intergenic (+87/‑383)yffL/yffMCPZ‑55 prophage; uncharacterized protein YffL/CPZ‑55 prophage; uncharacterized protein YffM
Reads supporting (aligned to +/- strand):  ref base C (12/11);  new base A (7/5);  total (19/16)
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

GGATCGGCAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAA  >  NC_000913/2560836‑2561134
                                                                                                                                                     |                                                                                                                                                     
ggATCGGCAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTc                                                                                                                                                       >  1:1413509/1‑150 (MQ=255)
ggATCGGCAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTc                                                                                                                                                       <  1:204182/150‑1 (MQ=255)
     ggCAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAATGGAGGGTAaaaat                                                                                                                                                  >  2:1098515/1‑149 (MQ=255)
           aaGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAATGGTGTGTCAAAAGttcacg                                                                                                                                            >  2:833471/1‑146 (MQ=255)
                aGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCTTTAAg                                                                                                                                       >  1:714595/1‑150 (MQ=255)
                   gCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTg                                                                                                                                    >  2:443224/1‑150 (MQ=255)
                   gCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTg                                                                                                                                    <  2:351432/150‑1 (MQ=255)
                   gCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTAAAAATTTGCCGTTAAGGTg                                                                                                                                    >  1:159050/1‑150 (MQ=255)
                      aCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATTGGTGGGTAAAAAGTTGAAGATAAggagtgt                                                                                                                                 >  1:1439445/1‑145 (MQ=255)
                         aaTACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGATGGGTAAAAAGTTGCCGTTAAGGAGGGTaaa                                                                                                                              >  2:2582/1‑150 (MQ=255)
                          aTACCAGTTATTATTCAAGCAGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTGCCGCCTTTTCTTTGCCTTAATTGCATGAATTCAGGTGGGTCAATAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCaaa                                                                                                                             <  2:1189163/150‑1 (MQ=255)
                            attaGTTATTATTTAATCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGGCTTTTATTTGCCTTAATTCCATGATTTAAGGTGGGTCAAAAGTTGCCGTTAGTTGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAg                                                                                                                           <  2:863848/147‑1 (MQ=255)
                                gTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGc                                                                                                                       >  1:1834608/1‑150 (MQ=255)
                                 ttattaTTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGcc                                                                                                                      <  2:1917859/150‑1 (MQ=255)
                                  tattatTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGTTGGGTAAAAAGTTGCCTTTAAGGTGGGTCAATATTTGcag                                                                                                                     >  1:1299294/1‑148 (MQ=255)
                                        tCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCTTTAAGGAGGGTCAAAAGTTGACGTTAAgg                                                                                                               >  2:1375468/1‑150 (MQ=255)
                                            gCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAATGGTGGGTAAAAAGTTGCCTTTTAGGAGGGTCAAATTTTGCAGAGAAGGTggg                                                                                                           >  2:1047983/1‑150 (MQ=255)
                                            cccGTACAACATGAAATAACGGAATCAGTCGTGCAATTTTACCTCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAATTTTGGCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTggt                                                                                                           <  2:645265/149‑2 (MQ=38)
                                                       tGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAATTTGCAGTAAAGGTGGGGCAAAAGTTGc                                                                                                >  1:1912296/1‑150 (MQ=255)
                                                           aTAACGGAATCAGGCGGGCACTGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAg                                                                                            <  1:554166/150‑1 (MQ=255)
                                                           aTAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAg                                                                                            <  1:600927/150‑1 (MQ=255)
                                                            tAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTAAAAATTTGCGGTTAAGGAGGGTGAAATTTTGAAGTGTAGGGGGGTGAAGAGTTggagact                                                                                           >  1:1822538/1‑144 (MQ=255)
                                                                       gtcGGGCAAATATCCCGCCTTTTCTATTCCATAATTCCATGAATTCAGGGTCGTCTAAATTAGCCGTTATTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTctac                                                                                <  1:633642/148‑1 (MQ=21)
                                                                        ccGGGCACTAATCCCGCCTTTCGTTTCCCTTAAATCAATGAATTCTGTGTCGTCAAAATTAGCCCTTACGGGTGGGTAATAAGCTGCCTTTAATGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTctact                                                                               <  2:117679/149‑1 (MQ=16)
                                                                           ggCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTTGTGGTGGGTCAAAAGTTGCCGTTAAGGAGGGTCAAAAGTTGCAGTTAAGGTGGGTCAAAAGTTGAGGAGTAAGAATTCTAGTAtt                                                                            >  2:476062/1‑150 (MQ=38)
                                                                           ggCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAATTTGCCGTTAAGGTGGGTCAAAAGTTGACGAGTAAGAATTCTACTAtt                                                                            >  1:3583/1‑150 (MQ=255)
                                                                           cgCAATTTTCCCGCCTTTTGTTTGCCTTAAATCCATGAATTCAGGTGGGTCAAAATCTGCCGTTATTGGTGGGTAAAAAGTTGCCTTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTAtt                                                                            <  1:833471/149‑1 (MQ=37)
                                                                              acttatCCCGCCTTTTGTTTGCCATATATCAATGAATTCAGTTTGCTAAAAATTTCCCTTTATTGTTGGGTAAAAAGTTGCCTTTTAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAg                                                                         <  2:1952611/145‑1 (MQ=21)
                                                                                    ccagCCATTTCTTTTCCTTAAATTCATGAATTCAGGCGGGTCAAAAGTAGCCCTTATGGGTGGGTCAAAAGATTCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCt                                                                   <  1:1830515/147‑1 (MQ=25)
                                                                                                        aTTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAGAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAg                                               >  1:829489/1‑150 (MQ=255)
                                                                                                        aTTCCATGAATTCAGGTGGGTCAAAAGTTCCCCTTTGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAg                                               <  1:2582/150‑1 (MQ=255)
                                                                                                        aTTACATGAATTCATTTGGCTAAAATTCTGTCTTTAGTTGTGGGTAAAAAGTTGCCTTTAATGTGGGTAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAg                                               <  2:3583/150‑1 (MQ=25)
                                                                                                                                 aGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAAGTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCg                      >  1:1151591/1‑150 (MQ=255)
                                                                                                                                            gtggtgGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTaa           >  1:821880/1‑150 (MQ=255)
                                                                                                                                              ggcgggTCATAAGTTCCCCTTATGGCGCGTCAAAAGTTTCCTTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAAc         <  1:648714/147‑1 (MQ=38)
                                                                                                                                                 gggTAAAAAGTTGCCTTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACaga      <  1:1191631/150‑1 (MQ=255)
                                                                                                                                                    tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACagaaga   >  2:1952112/1‑150 (MQ=255)
                                                                                                                                                     cAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAgaagaa  >  2:1179017/1‑150 (MQ=255)
                                                                                                                                                     cAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAgaacaa  >  2:884820/1‑150 (MQ=255)
                                                                                                                                                     |                                                                                                                                                     
GGATCGGCAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAA  >  NC_000913/2560836‑2561134

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: ‑