Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,502,887:1 (A)5→6 100% coding (1411/2106 nt) USA300HOU_2364 → AraC transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,502,8821.A93.3% 90.4 / 0.3 30coding (1406/2106 nt)USA300HOU_2364AraC transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base . (0/2);  new base A (15/13);  total (15/15)
Fisher's exact test for biased strand distribution p-value = 4.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
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.

TTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGTCTGTAAG  >  CP000730/2502747‑2503017
                                                                                                                                        |                                                                                                                                         
ttaaaaACAAAAATAAAGAAATTAAATATAGTGTGCCTGTTCAAGACTTTTTTTATAGGTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCaaaaa                                                                                                                                     >  1:390769/1‑141 (MQ=255)
  aaaaaCAAAAATAAAGAAATTAAATCTAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCCTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCaaacaaa                                                                                                                                    >  2:151390/1‑137 (MQ=255)
   aaaaCAAAAATAAAGAAATTAAATATAGTGTGACAGTCTATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATAATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCaaaaaact                                                                                                                                  >  1:27507/1‑138 (MQ=255)
     aaCAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCaaaaaactgc                                                                                                                                <  1:2866/141‑6 (MQ=255)
             tAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATc                                                                                                                        >  1:379073/1‑141 (MQ=255)
                 gAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTAt                                                                                                                    >  1:33923/1‑141 (MQ=255)
                     ttAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACt                                                                                                                >  2:83794/1‑141 (MQ=255)
                     ttAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATACAAAAAACTGCAACACATCTTATCACt                                                                                                                >  2:136091/1‑141 (MQ=255)
                        aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTaaa                                                                                                             <  1:254483/141‑1 (MQ=255)
                          tataGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTaaaaa                                                                                                           <  1:119495/141‑1 (MQ=255)
                                     aGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTatc                                                                                                >  2:227399/1‑141 (MQ=255)
                                                ttttAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGac                                                                                     <  1:254194/141‑1 (MQ=255)
                                                  ttAGAAACTTATTCAACCGTGGAACAAGTTCATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGacac                                                                                   <  2:248354/141‑1 (MQ=255)
                                                   tAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCAATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTCTCACTAAAAACCAACTATATCATCAGACTGCCACt                                                                                  >  1:11878/1‑141 (MQ=255)
                                                   tAGAAACTTACGCAAACGTAGAACAAGTTTATCCTCTCAAGCAACGTCTTAAATTCCATTATGACTTTATTGAAAAAAAAAAAAAAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACt                                                                                  <  2:381135/141‑1 (MQ=255)
                                                    aGAAACTTCTTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCCTAAATTCCATTATTTCTTAATTAAGGTGGAAAATTAAAATAACTTGAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTc                                                                                 <  1:92721/141‑1 (MQ=255)
                                                       aaCTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCAtt                                                                              <  1:55178/141‑1 (MQ=255)
                                                            aTTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGaa                                                                         >  1:344010/1‑141 (MQ=255)
                                                              tCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACa                                                                       >  2:234880/1‑141 (MQ=255)
                                                                 aCCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGta                                                                    >  1:375603/1‑141 (MQ=255)
                                                                       gAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATAGAAAATTAAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGaa                                                              <  2:165295/141‑1 (MQ=255)
                                                                         aCAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAat                                                            >  1:665/1‑141 (MQ=255)
                                                                         aCAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAat                                                            >  2:387552/1‑141 (MQ=255)
                                                                             gTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACCCATTTTGAACAGTATAAGAAatttat                                                        >  1:82559/1‑141 (MQ=255)
                                                                                      gtccggccccctCTTAAACTCCATTATGACTTGACTGATATTGAAAATTCAAAAAACTGCCACACACCTTATACCTATAAACCAACACTATTATCAAACTCACACTCATTTTGAACATTATAAGAAATTTATTTTAGATTc                                               <  2:239429/130‑1 (MQ=255)
                                                                                      gTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTc                                               <  1:162060/141‑1 (MQ=255)
                                                                                       tCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCa                                              >  1:256251/1‑141 (MQ=255)
                                                                                         aTGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAgg                                            <  1:207358/141‑1 (MQ=255)
                                                                                            cAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGtat                                         >  2:47300/1‑141 (MQ=255)
                                                                                              tcttCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTatat                                       <  2:66697/138‑1 (MQ=255)
                                                                                                  cTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATatcatc                                   <  1:351095/141‑1 (MQ=255)
                                                                                                   gtAAGTTCCATTATTCTATTATTGTCATTGAAAATTCAAAAAACTACGACTTTCCTTATCACTAAAAACCAACACTATCATCAAACTGACCCTCATTTTGAACAGTATAAGAAATTAATTTTAGATTCAGGTATAtcatca                                  <  2:196302/140‑1 (MQ=255)
                                                                                                                     ttATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATataat                >  2:184452/1‑141 (MQ=255)
                                                                                                                                   aaTTCAAAAACCTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGTCTGTAAg  <  1:302723/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                         
TTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGTCTGTAAG  >  CP000730/2502747‑2503017

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: