Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,063,805:1 +T 72.3% coding (684/1218 nt) USA300HOU_1000 ← LytR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,063,8041.T72.3% 106.4 / 45.9 47coding (685/1218 nt)USA300HOU_1000LytR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base . (9/4);  new base T (19/15);  total (28/19)
Fisher's exact test for biased strand distribution p-value = 5.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.51e-01

ATTTCAACATCATTTGTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTAT  >  CP000730/1063665‑1063938
                                                                                                                                              |                                                                                                                                      
aTTTCAACATCATTTGTTAAGTACGTTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAAt                                                                                                                                       >  1:486446/1‑141 (MQ=255)
       catcatTTGTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATtaaaatt                                                                                                                                >  1:96309/1‑138 (MQ=255)
            tttGTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCttaat                                                                                                                            <  1:599274/141‑1 (MQ=255)
               gTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTATTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACATCCTGTGCTTTTTGGAATTAAAATCttaattaa                                                                                                                         >  2:371175/1‑141 (MQ=255)
                             tGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGtt                                                                                                           >  2:463594/1‑141 (MQ=255)
                             tGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAACATCTTAATTAATTCCCTTTAACGttt                                                                                                          >  1:240103/1‑140 (MQ=255)
                                 aaaGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAAGAGAATCAACTTCCCGGGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTcc                                                                                                       <  1:140847/141‑1 (MQ=255)
                                 aaaGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCAGTTGTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTcc                                                                                                       <  1:621101/141‑1 (MQ=255)
                                  aaGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTcga                                                                                                      >  2:231635/1‑139 (MQ=255)
                                   aGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCAc                                                                                                     <  2:233026/141‑1 (MQ=255)
                                     cTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGt                                                                                                   <  2:141770/141‑1 (MQ=255)
                                       ttAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTTTTTTTTTTTTCTTAATTAATTCCATTTGACGTTGTTCACGttt                                                                                                 >  2:600471/1‑141 (MQ=255)
                                       ttAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGttt                                                                                                 >  2:364813/1‑141 (MQ=255)
                                       ttAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGatt                                                                                                 >  2:512932/1‑141 (MQ=255)
                                        tAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGtttt                                                                                                >  2:252133/1‑141 (MQ=255)
                                           tttCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTCATTAATTACATTTGACGTTGTCCACGTTTTCAg                                                                                             >  2:649001/1‑141 (MQ=255)
                                           tttCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTAAAg                                                                                             >  2:442087/1‑141 (MQ=255)
                                                  gttagttaAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATc                                                                                     >  1:574452/1‑141 (MQ=255)
                                                   ttagttaAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATc                                                                                     >  2:382579/1‑141 (MQ=255)
                                                      gttaAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCatga                                                                                 >  2:362106/1‑141 (MQ=255)
                                                        taAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCatgat                                                                                <  2:659788/141‑1 (MQ=255)
                                                         aaaTTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCatgatg                                                                               >  1:655419/1‑141 (MQ=255)
                                                         aaaTTATGCTTTCCATTGTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATATAATCAACTTCCTGTGCTTTTTAGAATTAAAATATTAATTAATTCCACTTTACGTTGTCAACGTTTAACGTCTGCATctagctg                                                                               >  2:55877/1‑135 (MQ=255)
                                                                        tttttACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTACGTCTGAATCATGATGTGTAGTTCTAGCaaa                                                                >  2:481214/1‑140 (MQ=255)
                                                                        tttttACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACt                                                               >  1:364292/1‑141 (MQ=255)
                                                                         ttttACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACt                                                               >  1:143792/1‑141 (MQ=255)
                                                                         ttttACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTg                                                              >  2:667076/1‑141 (MQ=255)
                                                                          tttACCTACAATTTGAATCACGTTATAAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTg                                                              >  2:113655/1‑141 (MQ=255)
                                                                                    aTTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCtc                                                    <  1:115023/141‑1 (MQ=255)
                                                                                    aTTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCtc                                                    <  1:173533/141‑1 (MQ=255)
                                                                                     tctGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTTCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCtca                                                   <  1:411691/139‑1 (MQ=255)
                                                                                          aTCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTACAATCTTAATTAATTCCATTTGACATTGTCCACGTTTTATGTCCGAATCATGATGTCTCGTTGTGGCAACTGCTCACCACTCATCAcc                                              >  1:169297/1‑141 (MQ=255)
                                                                                          aTCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCAcc                                              <  2:284348/141‑1 (MQ=255)
                                                                                          aTCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCAcc                                              >  2:56023/1‑141 (MQ=255)
                                                                                          aTCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCa                                             <  2:361726/141‑1 (MQ=255)
                                                                                                      aGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTgg                                 <  1:83579/141‑1 (MQ=255)
                                                                                                         ttATCAATAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTa                               <  2:293885/141‑1 (MQ=255)
                                                                                                         ttATCAATAGAAGCAACTTCCTTGTCTTTTGTGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTCTTAAGCCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTa                               <  2:201609/141‑1 (MQ=255)
                                                                                                                tAGAATCAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTAAATTGGGATGGGTACAACCGTGGTGGTTAAATCATGATGTCTGGTTCTGGCAACGGCTAAAGCCTCATCGCCATGTAATTTTTGGTACCCtttt                        >  1:657260/1‑141 (MQ=255)
                                                                                                                tAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCttttt                       >  2:595111/1‑141 (MQ=255)
                                                                                                                 aGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCtttttt                      <  2:259525/141‑1 (MQ=255)
                                                                                                                      cAACTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTttttaatt                  <  1:252133/141‑1 (MQ=255)
                                                                                                                       aaCTTCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTttttaattt                 <  1:308086/141‑1 (MQ=255)
                                                                                                                        aCTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTttttaatttta               >  2:91031/1‑141 (MQ=255)
                                                                                                                           tCCTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTttttaattttact             >  2:289717/1‑139 (MQ=255)
                                                                                                                            ccTGTGCTTTTTGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATc            >  1:640477/1‑141 (MQ=255)
                                                                                                                                        ttGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTat  <  2:650263/141‑1 (MQ=255)
                                                                                                                                        ttGGAATTAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTat  <  2:462950/141‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                      
ATTTCAACATCATTTGTTAAGTACATTTTTGCTAAAGCTTTAATTTCAGAGTTAGTTAAATTATGCTTTGCATTTTTACCTACAATTTGAATCACGTTATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTAT  >  CP000730/1063665‑1063938

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: