Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,063,912:1 +C 100% coding (577/1218 nt) USA300HOU_1000 ← LytR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,063,9091.C91.4% 109.2 / 6.1 35coding (580/1218 nt)USA300HOU_1000LytR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base . (1/2);  new base C (12/20);  total (13/22)
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
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

TAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAAT  >  CP000730/1063777‑1064043
                                                                                                                                     |                                                                                                                                       
tAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCctttt                                                                                                                                <  1:336138/141‑1 (MQ=255)
      cAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTttttaatt                                                                                                                           >  1:263241/1‑141 (MQ=255)
       aaCTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTttttaattt                                                                                                                          <  2:243259/141‑1 (MQ=255)
           tCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTtttaattttaat                                                                                                                      >  1:33529/1‑141 (MQ=255)
           tCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTtttaattttaat                                                                                                                      >  1:106372/1‑141 (MQ=255)
           tCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTtttttatttttctt                                                                                                                     >  2:16712/1‑137 (MQ=255)
           tCCTGTGCCTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTtttaattttaat                                                                                                                      <  1:108958/141‑1 (MQ=255)
                      ttGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTat                                                                                                           <  2:239481/141‑1 (MQ=255)
                         gAATATAATCTGAATTAATTCCATTTGACGTTGTCCAAGTTTAAATTCTGTATTATGATGTTTAGTTCTAGCAACTGCTAAAGCCTCATCATCATTTAATTTTTGGTACCCCTTTTTTGATTTTAATCTTACCAGTatcat                                                                                                        <  2:379048/141‑1 (MQ=255)
                                 tCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTa                                                                                                <  1:392009/141‑1 (MQ=255)
                                  tttaattaaTTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAg                                                                                               <  2:54339/140‑1 (MQ=255)
                                               aTTTGACCTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTc                                                                                  <  1:167936/141‑1 (MQ=255)
                                                tttGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCg                                                                                 >  1:37290/1‑141 (MQ=255)
                                                tttGACGTTGTCCACGTTTTAAGGCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCg                                                                                 <  1:64716/141‑1 (MQ=255)
                                                  tGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTa                                                                               <  1:294694/141‑1 (MQ=255)
                                                  tGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTa                                                                               <  2:236324/141‑1 (MQ=255)
                                                   gACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTAt                                                                              <  1:23996/141‑1 (MQ=255)
                                                               gTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTGTGGCACATCATAg                                                                  <  2:183758/141‑1 (MQ=255)
                                                                    aaGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCATATCATTGTatat                                                             <  2:46141/141‑1 (MQ=255)
                                                                     aGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATg                                                            >  1:231888/1‑141 (MQ=255)
                                                                     aGTCTGAATCATGATATCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAACTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATg                                                            >  1:294414/1‑141 (MQ=255)
                                                                                     tCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGCGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTa                                            >  2:359187/1‑141 (MQ=255)
                                                                                                ctaCTGCTAATGCCTCATCCCCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACa                                 <  2:75262/139‑1 (MQ=255)
                                                                                                 taCTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATCTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTATGTCGTATGGCACATCATAGTATCTGCCACCAAGCTCATTTACAGCCTCTACaa                                <  2:241116/140‑1 (MQ=255)
                                                                                                 aaCTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACaa                                <  2:33529/141‑1 (MQ=255)
                                                                                                 aaCTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCGCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTGAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACaa                                <  2:233565/141‑1 (MQ=255)
                                                                                                      cTAAAGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTTTTTTTTATCTTACCAGTATCAGCCGTGTTAGGTTCATTTTAGTCGTATTGCACATCATAGTATCTCCCACCAACCTCACTCACAGCCTCGCCACATGCt                           >  2:296553/1‑141 (MQ=255)
                                                                                                        aaaGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCttt                         >  1:20660/1‑141 (MQ=255)
                                                                                                          aGCCTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCa                       <  2:106372/141‑1 (MQ=255)
                                                                                                             cTCATCACCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCatat                    <  1:174828/141‑1 (MQ=255)
                                                                                                              tcatcaCCATTTAATTTTTGGTACCCCTTTTTTTTTTTTTTTCTTACCAGTATCATCTGTGTTAGTTTCATTTAAGTCTTATGGCACATCATAGTGTCTGCCACCAAGCTCTTTTACAGCCTCGACAATTGCTTTCATAtt                   >  2:118532/1‑141 (MQ=255)
                                                                                                              tcatcaCCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTCCCACAAACATCAATGAAAGGTTCATTAAAGTCGTATGGCACATCATAGAAAATACCACCAAACACATATACAGCCTCGACAAATGCTTTCATAtt                   >  1:34082/1‑141 (MQ=255)
                                                                                                              tcatcaCCATTTAATTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATAtt                   <  2:230046/141‑1 (MQ=255)
                                                                                                                          aaTTTTTGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGATCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATGGACTCTCACata       >  2:91441/1‑141 (MQ=255)
                                                                                                                               ttGGTACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATaataat  <  1:172741/141‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                       
TAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAAT  >  CP000730/1063777‑1064043

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: