Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,562,781 T→C 9.4% P366P (CCA→CCG)  lytN_2 ← putative cell wall hydrolase LytN

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,562,7810TC 9.4% 114.7 / 3.4 42P366P (CCA→CCG) lytN_2putative cell wall hydrolase LytN
Reads supporting (aligned to +/- strand):  ref base T (21/17);  new base C (2/2);  total (23/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.09e-01

ACATTAGCTACTGTGTAATTGCCTTGTTCTTTTTTATAAGGGACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAAGCGATAATTGATATTTATTTCTGCTGATACATTAA  >  USA300TCH1516_ALE/1562644‑1562920
                                                                                                                                         |                                                                                                                                           
aCATTAGCTACTGTGTAATTGCCTTGTTCTTTTTTATAAGGGACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGc                                                                                                                                          >  1:226267/1‑141 (MQ=255)
  aTTAGCTACTGTGTAATTGCCTTGTTCTTTTTTATAAGGGACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCtt                                                                                                                                        >  2:111734/1‑141 (MQ=255)
   ttAGCTACTGTGTAATTGCCTTGTTCTTTTTTATAAGGGACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTa                                                                                                                                       <  2:66290/141‑1 (MQ=255)
     aGCTACTGTGTAATTGCCTTGTTCTTTTTTATAAGGGACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCCATTGGCTTAcc                                                                                                                                     >  1:90227/1‑141 (MQ=255)
         aCTGTGTAATTGCCTTGTTCTTTTTTATAATGGACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCCCTAGCTACCACTCCACCAATTCGCTTACCacta                                                                                                                                 >  2:200452/1‑138 (MQ=255)
            gtgtAATTGCCTTGTTCTTTTTTATAAGGGACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATc                                                                                                                              >  1:155858/1‑141 (MQ=255)
             tgtAATTGCCTTGTTCTTTTTTATAAGGGACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCg                                                                                                                             <  2:243924/141‑1 (MQ=255)
                 aTTGCCTTGTTCTTTTTTATAAGGGACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCAcc                                                                                                                         >  1:38341/1‑141 (MQ=255)
                    gCCTTGTTCTTTTTTATAAGGGAGATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATCGGCTTACCATGAATCGCACCAGc                                                                                                                      >  1:124368/1‑141 (MQ=255)
                    gCCTTGTTCTTTTTTATAAGGGAGATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATCGGCTTACCATGAATCGCACCAGc                                                                                                                      >  1:335864/1‑141 (MQ=255)
                           tCTTTTTTATAAGGGACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGt                                                                                                               <  2:103195/141‑1 (MQ=255)
                           tCTTTTTTATAAGGGACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTCAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGt                                                                                                               >  1:104978/1‑141 (MQ=255)
                                   ataAGGGACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGAGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGATTACACTGAATGGCACCAGAGATTAGTTTAGGGTa                                                                                                       >  1:35037/1‑141 (MQ=38)
                                       gggACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAg                                                                                                   >  1:39310/1‑141 (MQ=255)
                                           gattattCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATCGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGt                                                                                               <  2:124368/140‑1 (MQ=255)
                                           gattattCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATCGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGt                                                                                               <  2:335864/140‑1 (MQ=255)
                                           cATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGt                                                                                               >  1:15638/1‑141 (MQ=255)
                                                            gtATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTaatccaa                                                                              <  2:223340/141‑1 (MQ=255)
                                                                aaCCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAatccaatcca                                                                          <  1:208039/141‑1 (MQ=255)
                                                                aaCCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAatccaatcca                                                                          <  1:251021/141‑1 (MQ=255)
                                                                    tgctgGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATc                                                                      >  1:225221/1‑141 (MQ=255)
                                                                     gctgGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCa                                                                     <  2:15638/141‑1 (MQ=255)
                                                                      gtgGAACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCAt                                                                    <  2:58628/140‑1 (MQ=255)
                                                                        ggCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCAttt                                                                  >  1:299574/1‑141 (MQ=255)
                                                                            cTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTttat                                                              >  1:15492/1‑141 (MQ=255)
                                                                             tGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTttatt                                                             >  2:356753/1‑141 (MQ=255)
                                                                                  gATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGtaa                                                        <  1:89736/141‑1 (MQ=255)
                                                                                       ttttCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATaaaa                                                   <  2:226267/141‑1 (MQ=255)
                                                                                          tCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATCTTTCTTAATCTAGTCCATATCATTTTTATTAGTAATAAAACCt                                                <  1:222187/141‑1 (MQ=255)
                                                                                              ttttAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAAtt                                            <  1:407595/141‑1 (MQ=255)
                                                                                                     tGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATaa                                     <  2:177385/141‑1 (MQ=255)
                                                                                                                ccgcACTAGCTATCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAAGCGATCAtttt                          <  2:175812/138‑3 (MQ=255)
                                                                                                                ccTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAAGCGATAATTGa                          <  1:19897/141‑1 (MQ=255)
                                                                                                                       aGCTACCACTCCACCAATTTGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAAGCGATAATTGAtatttat                   <  1:379451/141‑1 (MQ=255)
                                                                                                                          tACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAAGCGATAATTGATATTTATTTc                >  1:406382/1‑141 (MQ=255)
                                                                                                                          tACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAAGCGATAATTGATATTTATTTc                >  2:405231/1‑141 (MQ=255)
                                                                                                                          tACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAAGCGATAATTGATATTTATTTc                >  2:405248/1‑141 (MQ=255)
                                                                                                                             cACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAAGCGATAATTGATATTTATTTctgc             >  1:159262/1‑141 (MQ=255)
                                                                                                                               cTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAATCGATAATTCATATTTATTTctactg           >  2:261222/1‑141 (MQ=255)
                                                                                                                               cTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAAGCGATAATTGATATTTATTTctgctg           >  1:75375/1‑141 (MQ=255)
                                                                                                                                tCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAAGCGATAATTGATATTTATTTCTGCTGa          <  1:277211/141‑1 (MQ=255)
                                                                                                                                    ccaATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAAGCGATAATTGATATTTATTTCTGCTGATACa      >  2:37780/1‑141 (MQ=255)
                                                                                                                                        ttGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACATGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAAGCGATAATTGATATTTATTTCTGCTGATACATTaa  >  2:43335/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                           
ACATTAGCTACTGTGTAATTGCCTTGTTCTTTTTTATAAGGGACATTATTCTTATCGAGTGTATAACCTGCTGGCACTGGCGGATTCTTTTCGTTTTTAACTGGCGCTTTGACCTCACTAGCTACCACTCCACCAATTGGCTTACCATGAATCGCACCAGCTATTAGTTTAGAGTACAAGTCGTAATTTTTCTTAATCCAATCCATATCATTTTTATTAGTAATAAAACCTAATTCAGATAAGCGATAATTGATATTTATTTCTGCTGATACATTAA  >  USA300TCH1516_ALE/1562644‑1562920

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: ‑