Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,579,394 T→C 8.3% K121K (AAA→AAG)  USA300HOU_1446 ← hypothetical bacteriophage protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,579,3940TC 8.3% 130.0 / 3.2 48K121K (AAA→AAG) USA300HOU_1446hypothetical bacteriophage protein
Reads supporting (aligned to +/- strand):  ref base T (27/17);  new base C (2/2);  total (29/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.10e-01

GCTTCTGGGTTAAAAACTCCAACGTATAATCTTTTAAAACCTACTTTATAAGAACCTTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTTTGTTGATATAACAGGTATCTTATTCGTTTTGTTATATCAATTGTTTTC  >  CP000730/1579256‑1579532
                                                                                                                                          |                                                                                                                                          
gCTTCTGGGTTAAAAACTCCAACGTATAATCTTTTAAAACCTACTTTATAAGAACCTTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATAttttt                                                                                                                                          >  1:500513/1‑141 (MQ=255)
   tCTGGGTTAAAAACTCCAACGTATAATCTTTTAAAACCTACTTTATAAGAACCTTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTCTTggg                                                                                                                                       >  2:649988/1‑141 (MQ=255)
   tCTGGGTTAAAAACTCCAACGTATAATCTTTTAAAACCTACTTTATAAGAACCTTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTCTTggg                                                                                                                                       >  2:313396/1‑141 (MQ=255)
     tGGGTTAAAAACTCCAACGTATAATCTTTTAAAACCTACTTTATAAGAACCTTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTa                                                                                                                                     <  1:125762/141‑1 (MQ=255)
     tGGGTTAAAAACTCCAACGTATAATCTTTTAAAACCTACTTTATAAGAACCTTGTCCATCTTCATCTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTa                                                                                                                                     <  1:655917/141‑1 (MQ=255)
         ttAAAAACTCCAACGTATAATCTTTTAAAACCTACTGTATAAGAACCGTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGcc                                                                                                                                 >  1:304989/1‑141 (MQ=255)
           aaaaaCTCCAACGTATAATCTTTTAAAACCTACTTTATAAGAACCTTGTCCTTNTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGCTGCGATGCTTTTTCTAATATATATTTTTGGGTATGCCtt                                                                                                                               >  1:418434/1‑141 (MQ=255)
                     aCGTATAATCTTTTAAAACCTACTTTATAAGAACCTTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGCGTCTGCCTTGATATCGtct                                                                                                                     >  2:93214/1‑141 (MQ=255)
                     aCGTATAATCTTTTAAAACCTACTTTATAAGAACCTTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCGAGTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGtct                                                                                                                     >  2:367769/1‑141 (MQ=255)
                             tCTTTTAAAACCTACTTTATAAGAACCTTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATca                                                                                                             <  1:595454/141‑1 (MQ=255)
                                    aaaCCTACTTTATAAGAACCTTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACg                                                                                                      >  2:300024/1‑141 (MQ=255)
                                    aaaCCTACTTTATAAGAACCTTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACg                                                                                                      >  1:634553/1‑141 (MQ=255)
                                    aaaCCTACTTTATAAGAACCTGGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCCTGATATCGTCTCGACATCACATAACg                                                                                                      <  1:159614/141‑1 (MQ=255)
                                        cTACTTTATAAGAACCTTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATCACGTTTa                                                                                                  >  1:68409/1‑141 (MQ=255)
                                            tttATAAGAACCTTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGttt                                                                                              >  1:280095/1‑141 (MQ=255)
                                                          gTCCTTCAGCCATTGCTTAATTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCa                                                                                <  2:211003/141‑1 (MQ=255)
                                                           tCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCAt                                                                               <  1:534678/141‑1 (MQ=255)
                                                           tCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCAt                                                                               <  2:465175/141‑1 (MQ=255)
                                                           tCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCAt                                                                               <  1:385520/141‑1 (MQ=255)
                                                           tCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCAt                                                                               >  2:339155/1‑141 (MQ=255)
                                                            ccTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAGTATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTTAAAATAAGCATc                                                                              >  2:428319/1‑141 (MQ=255)
                                                            ccTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATc                                                                              >  1:215944/1‑141 (MQ=255)
                                                               tCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCCACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTaa                                                                           >  2:296059/1‑141 (MQ=255)
                                                                    cATTGCTTATTTCCTCCTTAATAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGAc                                                                      <  1:427772/141‑1 (MQ=255)
                                                                    cATTGCTTATTCCCCCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGAc                                                                      <  1:607186/141‑1 (MQ=255)
                                                                     aTTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACt                                                                     >  1:317395/1‑141 (MQ=255)
                                                                     aTTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACt                                                                     <  1:275136/141‑1 (MQ=255)
                                                                      ttGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTa                                                                    >  1:199027/1‑141 (MQ=255)
                                                                       tGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTaa                                                                   >  1:183590/1‑140 (MQ=255)
                                                                            aTTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCt                                                              >  1:502862/1‑141 (MQ=255)
                                                                              ttCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCtta                                                            >  1:642241/1‑140 (MQ=255)
                                                                              ttCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTg                                                            >  1:528197/1‑141 (MQ=255)
                                                                                cctcctTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGaa                                                          >  2:362314/1‑141 (MQ=255)
                                                                                  tcctGAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAAtt                                                        <  1:244050/141‑1 (MQ=255)
                                                                                      taaaaattaaaaaGCACACCTATTCGATGCGCTGATTTTTATAATGTATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAAt                                                    >  2:108418/1‑141 (MQ=255)
                                                                                      taaaaattaaaaaGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAAt                                                    <  2:588162/141‑1 (MQ=255)
                                                                                           attaaaaaGCACACCTATTCTATGCGCTGATTTTTAGAATAGATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTttgt                                               <  1:228996/141‑1 (MQ=255)
                                                                                             tataaggCACCCCGATGCGATGTGCTGATTGTTATAGTGGATATTTTTGGTTATGCCTGTATATCGTCTCGACATCACATAACGTTTAGGTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTttgttg                                             <  2:349264/135‑1 (MQ=255)
                                                                                              aaaaaGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTCGATGCTTGAATTAAATTttgttgt                                            >  1:13934/1‑140 (MQ=255)
                                                                                                aaaGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTTTGTTGata                                          >  1:18284/1‑141 (MQ=255)
                                                                                                         cTATTCGCTGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTTTGTTGATATAACAGGTa                                 <  2:201839/141‑1 (MQ=255)
                                                                                                            ttCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTTTGTTGATATAACAGGTATCt                              <  2:90507/141‑1 (MQ=255)
                                                                                                            ttCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAAAATAGTTGATATAACAGGTGTCt                              >  2:602840/1‑141 (MQ=255)
                                                                                                             tCGATGCGCTGATTTTTATAATATATATTCTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTTTGTTGATATAACAGGTATCtt                             <  1:649988/141‑1 (MQ=255)
                                                                                                             tCGATGCGCTGATTTTTATAATATATATTCTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTTTGTTGATATAACAGGTATCtt                             <  1:313396/141‑1 (MQ=255)
                                                                                                              cGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTTTGTTGATATAACAGGTATCTTa                            >  1:539552/1‑141 (MQ=255)
                                                                                                                  gcgcTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTTTGTTGATATAACAGGTATCTTATTCg                        >  1:528604/1‑141 (MQ=255)
                                                                                                                  gcgcTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTTTGTTGATATAACAGGTATCTTATTCg                        >  1:650382/1‑141 (MQ=255)
                                                                                                                      tGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGTTTGAATTAAATTTTGTTGATATAACAGGTATCTTATTCGtttt                    >  2:287062/1‑141 (MQ=255)
                                                                                                                                        tttttGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTTTGTTGATATAACAGGTATCTTATTCGTTTTGTTATATCAATTGTTTTc  <  1:435567/141‑1 (MQ=255)
                                                                                                                                        tttttGGGTACGCCTTGATCTCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTTTGTTGATATAACAGGTATCTTATGCGTTTTGTTATATCAATTGTTTTc  <  1:426240/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                          
GCTTCTGGGTTAAAAACTCCAACGTATAATCTTTTAAAACCTACTTTATAAGAACCTTGTCCTTCTGCCATTGCTTATTTCCTCCTTAAAAATTAAAAAGCACACCTATTCGATGCGCTGATTTTTATAATATATATTTTTGGGTATGCCTTGATATCGTCTCGACATCACATAACGTTTAGTTTCTTCAAAATAAGCATCTAACTGACTAGATGCTTGAATTAAATTTTGTTGATATAACAGGTATCTTATTCGTTTTGTTATATCAATTGTTTTC  >  CP000730/1579256‑1579532

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑