Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 3,652 T→A 17.4% intergenic (+336/‑45) dnaN → / → USA300HOU_0003 DNA‑directed DNA polymerase beta subunit/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007303,6520TA17.4% 87.2 / 2.3 42intergenic (+336/‑45)dnaN/USA300HOU_0003DNA‑directed DNA polymerase beta subunit/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (17/17);  new base A (2/6);  total (19/23)
Fisher's exact test for biased strand distribution p-value = 2.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAAGTTGAATATAAAAGTTAAACGCCGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCA  >  CP000730/3525‑3788
                                                                                                                               |                                                                                                                                        
cAAGGTGAATATAAAAGTTAAACGCCGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGt                                                                                                                             <  1:335472/141‑1 (MQ=255)
  aGTTGAATATAAAAGTTAAACGCCGTTAAATAGCGTTAAAAAATTGAAAATGAAAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAAAGGTTTCTACCTATATTTTAAATGAAATATGAGACAGAAAAAGatat                                                                                                                           >  2:180185/1‑141 (MQ=255)
  aGTGGAATATAAAAGTTAAACGCCGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGtaa                                                                                                                           >  2:47223/1‑140 (MQ=255)
    ttGAATATAAAAGTTAAACGCCGTTAGATAGCGTTAAAAAATTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTGATATGCAAACGGTTTCTACCTCTATTTTAAATGAAATCTGTGACAAAAAAAGGTataa                                                                                                                         <  1:233419/141‑1 (MQ=255)
    ttGAATATAAAAGTTAAACGCCGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTataa                                                                                                                         <  1:105047/141‑1 (MQ=255)
    gtGAATATAAAAGTTAAACGCCGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTataa                                                                                                                         <  2:265624/140‑1 (MQ=255)
      tagtataAAAGTTAAACGTCGTTAAATAGCGTTAAAAAATTGAAAATGCCAGTATTGCCAAAAAATAAGACTTAATTATTTATATGTAAACGGTTTCGACCTCTATTTTAAATGAAATTTGTTACAAAATAAGGTataata                                                                                                                       <  2:162424/138‑1 (MQ=255)
       aaTATAAAAGTTAAACGCCGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAatat                                                                                                                      >  2:184866/1‑141 (MQ=255)
       aaTATAAAAGTTAAACGCCGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTACTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAatat                                                                                                                      >  2:269279/1‑141 (MQ=255)
                aatAAACAACGTTAAATAGCGTTAAAAAATTGAAAAGGAAAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAAAAAAAAAAAAAAAAAGGTATAATATATTAATGAc                                                                                                             <  2:30010/139‑1 (MQ=255)
                   aaaCGCCGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATGGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATATTAAATGAAATTTGTGACAAAAAAAGGTATAATATCATAATGACATa                                                                                                          >  1:172797/1‑141 (MQ=255)
                    aaCGCCGTTGAATAGCGTTAAAGAAGTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACAtca                                                                                                         >  2:129691/1‑139 (MQ=255)
                     aCGCCGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACa                                                                                                        <  1:263904/141‑1 (MQ=255)
                        ccGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAg                                                                                                     >  1:316932/1‑141 (MQ=255)
                         cGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGAC‑AAAAAAGGTATAATATATTAATGACATACAAAGaa                                                                                                   >  2:371529/1‑141 (MQ=255)
                         cGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATTACCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATAAAATTTGTGACAAAAAAAGGTGTGATATATTAGTGACATAAAAAGa                                                                                                    >  2:294293/1‑141 (MQ=255)
                                  gCGTTAAAAAATTTAAAATGACATTATTTCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACATCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTg                                                                                           <  2:286489/141‑1 (MQ=255)
                                        aaacaTTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTCCTGCCTCTATTTTAAATGAACTTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGCAATgagcagcagctt                                                                                     >  2:313864/1‑130 (MQ=255)
                                        aaaaaTTGAAAACGACAGTAATGCCAAAAAATAAGAATTAATCATTTATATGTAAACGATTTCTACCTCTATTTTAAATGAAAAAAAAAAAAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGattatt                                                                                     <  2:350306/141‑1 (MQ=255)
                                                  aaTGACAGTACTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCaag                                                                           <  1:80135/141‑1 (MQ=255)
                                                   aTGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCgaga                                                                          >  1:202035/1‑141 (MQ=255)
                                                    agaaaGTATGGCAAAAAAATAAGAATTAATTATTTATATGTAAACGATTTCTACCTCTATTTTAAATGAAAAAAAAAAAAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCaagaa                                                                         <  2:341784/137‑1 (MQ=255)
                                                     gagagaatggCCAAAAAATAATAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAAAAAAAAAAAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCaagaag                                                                        <  2:191962/132‑1 (MQ=255)
                                                     gACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAATCGGTTTCTAGCTCTATTTTAAATGAAATTTGAGAAAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCaagaag                                                                        <  2:193552/141‑1 (MQ=255)
                                                         gTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTgt                                                                    <  1:166999/141‑1 (MQ=255)
                                                              gCCAAAAAATAAGAATTAATGATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTGTAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGtagtag                                                               <  2:217954/141‑1 (MQ=255)
                                                                     aaTAAGAATTAATTATTTATATGTAAATGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGgaga                                                        <  1:133132/141‑1 (MQ=255)
                                                                     aaTAAGAATTAATTATTGATATGTAAACGGTTTCTACCTCTATTTTAAACGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAATAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGgaga                                                        <  1:133088/141‑1 (MQ=255)
                                                                       aaaGAATTAATTATTTATACGGAAACGGTTTCTAACTCTATTTTAAATTAAAAAAAAAAAAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACa                                                      <  2:26874/140‑1 (MQ=255)
                                                                        aaGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTGGTAGTAGAAGGAGACAt                                                     >  2:320698/1‑141 (MQ=255)
                                                                        aaGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGAC‑AAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACAtt                                                    <  1:371529/141‑1 (MQ=255)
                                                                         acaattaattATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGGAGTGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACAtt                                                    >  1:298474/3‑141 (MQ=255)
                                                                                 ttatttatATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGAAGTGATAATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAgg                                            >  2:89544/1‑141 (MQ=255)
                                                                                        tatGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGAGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAAttt                                     >  2:142960/1‑141 (MQ=255)
                                                                                            tAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTaa                                 <  1:64595/141‑1 (MQ=255)
                                                                                                     acgaCCTCGATGTTAAATGAAATATGAGACAACAAAAGGTATAATATATTAATGACCTACAAAGAAATGGAGTGATTATTTTGTTTCAAGAAGTAGGAGTAGAAGGAGACATTACTTTAGGTCAATTTCTAGAAACAGAAg                        >  2:47224/4‑141 (MQ=255)
                                                                                                       tACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAggg                      >  1:352652/1‑141 (MQ=255)
                                                                                                        aCCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGa                     >  2:22231/1‑141 (MQ=255)
                                                                                                                    aaTGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCtg         >  1:5131/1‑141 (MQ=255)
                                                                                                                         aaTTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTggtggt    <  1:289167/141‑1 (MQ=255)
                                                                                                                           tttGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCa  <  1:118155/141‑1 (MQ=255)
                                                                                                                           attGTGAAAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCa  <  2:162881/140‑1 (MQ=255)
                                                                                                                               |                                                                                                                                        
CAAGTTGAATATAAAAGTTAAACGCCGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATTGCCAAAAAATAAGAATTAATTATTTATATGTAAACGGTTTCTACCTCTATTTTAAATGAAATTTGTGACAAAAAAAGGTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCA  >  CP000730/3525‑3788

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑