Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,569,145 T→C 16.0% M447V (ATG→GTG)  USA300HOU_1439 ← hypothetical bacteriophage protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,569,1450TC16.0% 53.0 / 3.8 25M447V (ATG→GTG) USA300HOU_1439hypothetical bacteriophage protein
Reads supporting (aligned to +/- strand):  ref base T (17/4);  new base C (2/2);  total (19/6)
Fisher's exact test for biased strand distribution p-value = 2.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

ATAACTCGTCTGTTAAGTGCTTGTTGAATTTGTACCATATCTTTTATTTCATTGCTGAAAGACACTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTAACATCTAATTCAGTCTTAGGAGTATCATTTATTTGCTTTTTTGCAAATTCTAACAGCTTATCCTGTGTTTCGATATCTT  >  CP000730/1569009‑1569285
                                                                                                                                        |                                                                                                                                            
aTAACTCGTCTGTTAAGTGCTTGTTGAATTTGTACCATATCTTTTATTTCATTGCTGAAAGACACTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATCTCCCATTAAt                                                                                                                                          >  1:204852/1‑141 (MQ=255)
    cTCGTCTGTTAAGTGCTTGTTGAATTTGTACCATATCTTTTATTTCATTGCTGAAAGACACTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCACTAATTCAt                                                                                                                                      >  1:21243/1‑141 (MQ=255)
    cTCGTCTGTTAAGTGCTTGTTGAATTTGTACCATATCTTTTATTTCATTGCTGAAAGACACTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCACTAATTCAt                                                                                                                                      >  1:20890/1‑141 (MQ=255)
          tGTTGAGTGCTTGTTGAATTTGTACCATATATTTTATTTCATTGCTGAAAGACACTTCATCTATTGCGTTTACAAATGGATGTGACCTATCTAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACag                                                                                                                                >  2:164334/1‑140 (MQ=255)
           gTTAAGTGCTTGTTGAATTTGTACCATATCTTTTATTTCATTGCTGAAAGACACTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACaaa                                                                                                                               >  2:232993/1‑141 (MQ=255)
                   cTTGTTGAATTTTTACCATATCTTTTATTTCATTGCTGAAAGACACTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACGc                                                                                                                       <  2:269871/141‑1 (MQ=255)
                            tttGTACCATATCTTTTATTTCATTGCTGAAAGACACTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACGCTATCTCTTg                                                                                                              <  1:270069/141‑1 (MQ=255)
                             ttGTACCATATCTTTTATTTCATTGCTGAAAGACACTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAACTACGCTATCTCTTgg                                                                                                             >  2:209236/1‑141 (MQ=255)
                                      atCTTTTATTTCATTGCTGAAAGACACTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCACTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTAtttt                                                                                                    <  2:21243/141‑1 (MQ=255)
                                      atCTTTTATTTCATTGCTGAAAGACACTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCACTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTAtttt                                                                                                    <  2:20890/141‑1 (MQ=255)
                                               ttCATTGCTGAAAGACACTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAAcc                                                                                           <  1:208400/141‑1 (MQ=255)
                                                           aGACACTTCATCTATTGCGTTTACAAATGGCTGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACGCTCTCGCTTGGCTCTATTTTTTCATAACCTATATAATTAAc                                                                               >  1:246145/1‑141 (MQ=255)
                                                              cacTTCATCTATTGCGTTTACAAATGGCTGTCACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTAACATc                                                                            >  2:178943/1‑141 (MQ=255)
                                                              cacTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTGATAACCTATATAATTGACATc                                                                            >  1:176908/1‑141 (MQ=255)
                                                              cacTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTAACATc                                                                            >  2:191445/1‑141 (MQ=255)
                                                              cacTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTGTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACTCATATAATTTACATc                                                                            >  1:7318/1‑141 (MQ=255)
                                                                          tGCGTTTACAAATGGATGTTATCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACTCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTAACATCTAATTCAGTCtt                                                                <  2:107729/141‑1 (MQ=255)
                                                                                    aaTGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGTACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTAACTTCTAATTCAGTTTTAGGAGTTTCa                                                      >  2:208075/1‑141 (MQ=255)
                                                                                                    cAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTAACATCTAATTCAGTCTTAGGAGTATCATTTATTTGCttttttt                                      >  1:188600/1‑140 (MQ=255)
                                                                                                         ttAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTAACATCTAATTCAGTCTTAGGAGTATCATTTATTTGCTTTTTTGCAAAt                                 >  2:220635/1‑141 (MQ=255)
                                                                                                         ttAACAACCTTTAATTCAGTGTATTAGCCCATTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTAACATCTAATTCAGTCTTAGGAGTATCATTTATTTGCTTTTTTGCAAAt                                 >  1:267379/1‑141 (MQ=255)
                                                                                                          tAACAACCTTTAATTCAGTGTTATATGCCATTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTAACATCTAATTCAGTCTTAGGAGTATCATTTATTTGCTTTTTTGCAAAtt                                >  2:167824/1‑141 (MQ=255)
                                                                                                          tAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTAACATCTAATTCAGTCTTAGGAGTATCATTTATTTGCTTTTTTGCAAAtt                                >  1:111704/1‑141 (MQ=255)
                                                                                                                                     ccATTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTAACATCTAATTCAGTCTTAGGAGTATCATTTATTTGCTTTTTTGCAAATTCTAACAGCTTATCCTGTGTTTCGatat     >  1:87188/1‑141 (MQ=255)
                                                                                                                                       aTTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTAACATCTAATTCAGTCTTAGGCGTATCATTTATTTGCTTTTTTGCTATTTCTAACAGCCTATCCTGTGTTTCGATATCt   >  2:42797/1‑141 (MQ=255)
                                                                                                                                        ttAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTACCATCTAATTCAGTCTTAGGAGTATCATTTATTTGCTTTTTTGCAAATTCTAACAGCTTATCCTGTGTTTCGATATCtt  >  2:166167/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                            
ATAACTCGTCTGTTAAGTGCTTGTTGAATTTGTACCATATCTTTTATTTCATTGCTGAAAGACACTTCATCTATTGCGTTTACAAATGGATGTGACCTATCAAGTTTAACAACCTTTAATTCAGTGTTATATCCCATTAATTCATGAACAAAAAATACGCTATCTCTTGGCTCTATTTTTTCATAACCTATATAATTAACATCTAATTCAGTCTTAGGAGTATCATTTATTTGCTTTTTTGCAAATTCTAACAGCTTATCCTGTGTTTCGATATCTT  >  CP000730/1569009‑1569285

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑