Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,344,530	G→A	7.1%	intergenic (+266/‑163)	USA300HOU_1253 → / → USA300HOU_1255	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,344,530	0	G	A	7.1%	146.4 / 3.2	56	intergenic (+266/‑163)	USA300HOU_1253/USA300HOU_1255	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (30/22);  new base A (2/2);  total (32/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.73e-01

TATGTTGCCAAAATAGATAGTAAAACATCTAAATTATGTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTAAAAATGGTAAAATAAAAATAGAAAT  >  CP000730/1344392‑1344666                                                                                                                                             |                                                                                                                                         taggTTGCCAAAATAGATAGTAAAACATCTAAATTATGTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCCAACATGt                                                                                                                                         <  1:167927/138‑1 (MQ=12)   tGTTGCCAAAATAGATAGTAAAACATCTAAATTATGTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTgg                                                                                                                                      <  2:453273/141‑1 (MQ=35)       gCCACAATAGATGGTAAAACATCTAAATTATGTCATTCACTTAACGCAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTAAGCATCTTT‑GGTGTAGAAGTACCACAGTACC‑ACATGTTGGCCAt                                                                                                                                  >  1:402615/1‑141 (MQ=11)            aaTAGATAGTAAAACATCTAAATTCTGTCCCTCACTTAACGGAAAAATAATTAAAGTTAAAGATATGATACCAGGTGTGAATACGCCACCTATGCATCCTT‑GGTGTAGAAGTACAACAGTGCC‑CCATGTTGGCAATTGGCg                                                                                                                             >  2:237948/1‑141 (MQ=11)            aaTAGATAGTAAAACATCTAAATTATGTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCACGTGGGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCg                                                                                                                             >  2:487594/1‑141 (MQ=25)              tagatagTAAAACATCTAAATTATGTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGGGCAAACTATGCATCCTT‑GGTGTAGAAGTACCACAGTGAC‑ACATGTTGGCACTTGGCggg                                                                                                                           >  1:131437/1‑141 (MQ=11)              tagatagTAAAACATCTAAATTATGTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACGTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCggg                                                                                                                           <  2:348787/141‑1 (MQ=37)              tagatagTAAAACATCTAAATTATGTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCggg                                                                                                                           <  1:532089/141‑1 (MQ=38)              tagatagTAAAACATCTAAATTATGTCATTCACCTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑TCATGTTGGCAATTGGCggg                                                                                                                           <  2:318977/141‑1 (MQ=255)                gatagTAAAACATCTAAATTATGTCATTCACTTAACGGAACAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACAACAGTGCC‑ACATGTTGGCAGTTGGCggggc                                                                                                                         >  1:226628/1‑139 (MQ=255)                gatagTAAAACATCTAAATTATGTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTATAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGaa                                                                                                                         >  2:117406/1‑140 (MQ=38)                   agTAAAACATCTAAATTATGTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGC‑TCTTTAGCTGCAGAAGGACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAg                                                                                                                      >  1:325956/1‑141 (MQ=11)                      aaaaCATCTAAATTATGTCATTCACTTAACGGAAAAAGATTTAAAGTTAAAGAGATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTc                                                                                                                   <  1:75637/141‑1 (MQ=255)                            tCTAAATTATGTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTaaa                                                                                                             >  2:40153/1‑141 (MQ=38)                            tCTAAATTATGTCATTCACGTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGGGCC‑ACATGTTGGCACTTGGGGGGACAAGTTCTTTaaa                                                                                                             >  2:523470/1‑141 (MQ=255)                               aaaTTATGTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAagag                                                                                                          <  1:482181/141‑1 (MQ=38)                                  ttATGTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGt                                                                                                       <  1:31182/141‑1 (MQ=38)                                      gTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATCTGATACCAGGTGTGAATGCGCCACATATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAg                                                                                                   >  2:102112/1‑141 (MQ=255)                                       tCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCCT‑GATTCAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGCCAAGTTCTTTAAAGAGCGTGAAgg                                                                                                  >  1:272799/1‑141 (MQ=14)                                         aTTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGGGTGAAGGTa                                                                                                >  2:418547/1‑141 (MQ=38)                                            cACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAat                                                                                             >  1:527134/1‑141 (MQ=38)                                               ttAAGGGAAAAATATTTAAAGTTAAAGATATGAGACCTGGTGCGAAGGCGCGACCTAGGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGATCGTGAAGGTAAatacc                                                                                          <  2:259452/141‑3 (MQ=11)                                                             tttAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGCGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGCGCCAGAAGGTAAATATCTATTAGAAGTaaaa                                                                            >  2:121687/1‑141 (MQ=14)                                                             tttAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGCGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGAGACAAGTTCGGTACAGAGCGTGAAGGTAAATAGCAAGTAGAAGTaaaa                                                                            >  2:517606/1‑141 (MQ=11)                                                                aaagttaaagATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTCGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAaagaa                                                                         >  1:534162/1‑141 (MQ=255)                                                                  agttaaagATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGc                                                                       >  1:189537/1‑141 (MQ=255)                                                                   gttaaagAAATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGCACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCa                                                                      <  2:331244/141‑1 (MQ=255)                                                                      aaagATATGATACCAGGTGTGAATGCGCCCCCTATGCATCGTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATaa                                                                   <  2:2153/141‑1 (MQ=255)                                                                       aagATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAATTAAAAGAAGCaggat                                                                  >  1:129244/1‑137 (MQ=255)                                                                          atatTAGACCAGGTTGGAATGCGCCACCTATGTCTCCTT‑GGTGTAGAAGTTCCTTAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGTTAAATATCAAGTAGAAGTAAAAGAAGCATAATTAc                                                               <  2:213714/141‑1 (MQ=17)                                                                            atGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAg                                                             <  2:105044/141‑1 (MQ=255)                                                                              gATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGa                                                           <  1:520808/141‑1 (MQ=255)                                                                                      gtgtGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAACAGCTa                                                   >  2:274095/1‑141 (MQ=255)                                                                                      gtgtGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTGGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTa                                                   >  1:252357/1‑141 (MQ=255)                                                                                      gtgtGAATGCGCCACCTATGCATCCCT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGCCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCATGAAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTa                                                   >  2:129331/1‑141 (MQ=255)                                                                                         tgAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTaaaa                                                >  1:167985/1‑141 (MQ=255)                                                                                               cgcCAACTATGCATCCTT‑GGTGCAGGAGTACCACAGTGCC‑ACGTGTTGGCAATTGGCGGGAGAAGTTCTTTAAAGAGCGTGAAGGTAAAGATCAAGTAGAAGTAAAAGAGGCATAATTACAGGAAAAAGCTAAAAACCAGa                                          <  2:203416/141‑1 (MQ=18)                                                                                                          cATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATg                               >  1:124745/1‑141 (MQ=255)                                                                                                           aTCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGa                              <  1:40153/141‑1 (MQ=255)                                                                                                               tt‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTaa                          >  1:527642/1‑141 (MQ=255)                                                                                                               tt‑GGTGGAGAAGTAACACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTaa                          <  2:301562/141‑1 (MQ=255)                                                                                                                  ggTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTaaaa                        >  1:288351/1‑141 (MQ=255)                                                                                                                  ggTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTaaaa                        >  1:444175/1‑141 (MQ=255)                                                                                                                   gtgtAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTaaaaa                       <  1:408672/141‑1 (MQ=255)                                                                                                                         aaGTACCACAGTGCC‑ACATATTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTAAAAATGGtaa                 >  2:395290/1‑141 (MQ=255)                                                                                                                         aaGTACCACAGTGCC‑ACATATTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTAAAAATGGtaa                 >  2:395206/1‑141 (MQ=255)                                                                                                                             aCCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTAAAAATGGtaaaata             >  2:300119/1‑141 (MQ=255)                                                                                                                               cacaGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTAAAAATGGtaaaataaa           >  2:88156/1‑141 (MQ=255)                                                                                                                                 caGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTAAAAATGGTaaaaaaaaaa         >  2:111167/1‑141 (MQ=255)                                                                                                                                     gCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGTGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTAAAAATGGTAAAATAAAAATAGa     <  2:71459/141‑1 (MQ=255)                                                                                                                                     gCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTAAAAATGGTAAAATAAAAATAGa     <  1:353014/141‑1 (MQ=255)                                                                                                                                       c‑acaTGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTAAAAATGGTAAAATAAAAATAGaaa   <  1:354805/141‑1 (MQ=255)                                                                                                                                       c‑acaTGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTAAAAATGGTAAAATAAAAATAGaaa   <  1:525114/141‑1 (MQ=255)                                                                                                                                       c‑acaTATTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTAAAAATGGTAAAATAAAAATAGaaa   <  1:395206/141‑1 (MQ=255)                                                                                                                                       c‑acaTATTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTAAAAATGGTAAAATAAAAATAGaaa   <  1:395290/141‑1 (MQ=255)                                                                                                                                         acaTGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCAAAATTACAGGGAAAAACTAAAAACCAGATGAAAGAAATGATTAAAAAAGGTAAAAtaaaaataaaaaa  >  2:344341/1‑140 (MQ=37)                                                                                                                                             |                                                                                                                                         TATGTTGCCAAAATAGATAGTAAAACATCTAAATTATGTCATTCACTTAACGGAAAAATATTTAAAGTTAAAGATATGATACCAGGTGTGAATGCGCCACCTATGCATCCTT‑GGTGTAGAAGTACCACAGTGCC‑ACATGTTGGCAATTGGCGGGACAAGTTCTTTAAAGAGCGTGAAGGTAAATATCAAGTAGAAGTAAAAGAAGCATAATTACAGGAAAAAGCTAAAAACCAGATGAAAGAAATGATTAAAAATGGTAAAATAAAAATAGAAAT  >  CP000730/1344392‑1344666

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: ‑