Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	745,728	A→G	16.8%	K9E (AAA→GAA)	USA300HOU_0690 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	745,728	0	A	G	16.8%	55.8 / 6.0	29	K9E (AAA→GAA)	USA300HOU_0690	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (11/13);  new base G (3/2);  total (14/15)
Fisher's exact test for biased strand distribution p-value = 6.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01

ACAGTTTGAAGAAATCGTAGTTCAATAATGTTAATTGTGAAAATGTAT‑‑‑‑‑‑ATAAACATAAAAAAATCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAATATATGCGAAATTTGGTAAGGAGATTTATGTTGCAGCAAAATCTGGTGAACCCAATCCAGAATCTAACCAAGCTTTAAGGTTGGTGCTTGA  >  CP000730/745590‑745858                                                                                                                                                 |                                                                                                                                   aCAGTTTGAAGAAATCGTAGTTCAATAATGTTAATTGTGAAAATGTAT‑‑‑‑‑‑ATAAACATAAAAAAATCATGTATAATATATGTTGTTAATTAACCAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTaa                                                                                                                                   <  2:431251/140‑1 (MQ=255)    gTTTGAAGAAATCGTAGTTCAATAATGTTAATTGTGAAAATGTAT‑‑‑‑‑‑ATAAACATAAAAAAATCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGa                                                                                                                                <  1:63932/140‑1 (MQ=255)       tGAAGAAATCGTATTTCAATAATGTTAATTGTGAAAATGTAT‑‑‑‑‑‑CTAAACATAAAAAAATCCTGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGaaac                                                                                                                             >  2:168098/1‑139 (MQ=255)              aTCTTAGTTAAATAATTTTAATTTTGAAAATGTAT‑‑‑‑‑‑ATAAACATAAAAAAATCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGcc                                                                                                                      <  2:422213/140‑1 (MQ=255)              aTCGTAGTTCAATAATGTTAATTGTGCAAATGTAT‑‑‑‑‑‑ATAAAGATAAAAAAATCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAGTGGAATCACATTAAAGAAAAAAAggga                                                                                                                      >  2:139961/1‑138 (MQ=255)              aTCGTAGTTCAATAATGTTAATTGTGAAAATGTAT‑‑‑‑‑‑ATAAACATAAAAAAATCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGcc                                                                                                                      <  1:204708/140‑1 (MQ=255)                     ttCAATCTTGTGAATTGTGAAAACGTAT‑‑‑‑‑‑ATAAACATAAAAAAATCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAg                                                                                                               <  2:377992/140‑1 (MQ=255)                            atGTTAATTGTGAAAATGTATATAAACATAAACATAAAAAAATCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGa                                                                                                              <  2:473983/140‑1 (MQ=255)                            atGTTAATTGTGAAAATGTATATAAAAATAAACAAAAAAAAATCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGa                                                                                                              <  2:473959/140‑1 (MQ=255)                                tAATTGTGAAAATGTAT‑‑‑‑‑‑ATAAACATAAAAAAATCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGAAGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGATaaaaaaaaa                                                                                                    >  1:521735/1‑136 (MQ=255)                                        aaaaTGTAT‑‑‑‑‑‑ATAAACATAAAAAAATCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAat                                                                                            >  1:298722/1‑140 (MQ=255)                                            tGTAT‑‑‑‑‑‑ATAAACATAAAAAAATCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTGAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAatatat                                                                                        >  2:458108/1‑140 (MQ=255)                                            tGTAT‑‑‑‑‑‑ATAAACATAAAAAAATCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTGAAAAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAatatat                                                                                        >  1:119176/1‑140 (MQ=255)                                                     aacataaCATAAAAAATTGATGTATAACTTATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAACGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAATATATGCg                                                                                     <  2:369400/135‑1 (MQ=255)                                                                aaaaaaTCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGAGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAATATATGAGCAACTTGGTaa                                                                          >  2:1217/1‑140 (MQ=255)                                                                  aaaaTCATGTATAATATATGTTGCTTCTAAATTAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTGAAGAAAAAAAGGCCCAAAGAGAGAAAAACACAAGTAGAATATATGCGAAATTTGAGAAgg                                                                        >  2:529353/1‑140 (MQ=255)                                                                       cATGAATAATATAATTTTATAATAAAACGTTTCAAAAGCGAGATAACATTATGGAACGTAAAAGAAATAACAATAAAAAAAAAAAGGCTCAAAAAGATAAAAACACAAGTAGATAACCGGCGTGAGTTGGTAAGGAGAtt                                                                   <  2:391155/140‑1 (MQ=255)                                                                         tGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAATATATGCGAAATTTGGTAAGGAGATTTa                                                                 >  1:312043/1‑140 (MQ=255)                                                                                 atatGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGATAAAAACACAATTAGAATATATGCGAAATTTGGTAAGGAGATTTATGTTgcag                                                         <  1:377213/140‑1 (MQ=255)                                                                                 atagGTTGTTAAGTAAACAGTTCGAAAGCGAGATGACATTGTGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCCAAAAGATTTAAACACAAGTAGAATATATGCGAAATTTGGTAAGGAGATTTATGTTgccg                                                         <  2:144060/140‑3 (MQ=255)                                                                                               aaaCAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAATATATGCGAAATTTGGTAAGGAGATTTATGTTGCAGCAAAATCTGGTGaa                                           >  1:115867/1‑140 (MQ=255)                                                                                               aaaCAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAATATATGCGAAATTTGGTAAGGAGATTTATGTTGCAGCAAAATCTGGTGaa                                           >  1:346846/1‑140 (MQ=255)                                                                                                     ttCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAATATATGCGAAATTTGGTAAGGAGATTTATGTTGCAGCAAAATCTGGTGAACCCAAt                                     >  1:528300/1‑140 (MQ=255)                                                                                                            gCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAATATATGCGAAATTTGGTAAGGAGATTTATGTTGCAGCAAAATCTGGTGAACCCAATCCAGAAt                              <  1:406693/140‑1 (MQ=255)                                                                                                             cGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCTCAAAAAGATAAAAACACAAGTAGAATATATGCGAAATTTGGTAAGGAGATTTATGTTGCAGCAAAATCTGGTGAAGCCAATCCAGAATc                             >  2:186080/1‑140 (MQ=255)                                                                                                                          tGGGACGTAAATGGAATAACATTAAAGGAAAAAAGGCGTAACAAGATCAAAACACAAGTAGAATATATGCGACATTTGGTAAGGAGATGTATGTTGCAGAAAAGTCTGGTGAACACAATACAGCATCTAAcacagcctga                >  2:471922/1‑131 (MQ=255)                                                                                                                                     tGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAATATATGCGAAATTTGGTAAGGAGATTTATGTTGCAGCAAAATCTGGTGAACCCAATCCAGAATCTAACCAAGCTTTAAGGTTGGTGCt     <  2:312043/140‑1 (MQ=255)                                                                                                                                      gtaacaaCATTAAAGAAAAAAAGGCCCAAAAAGATAACAACACACGTAGGATATATGCGAAATTTGGTAAGGAGATTTATGTTGCAGCAAAATCTGGTGAACCCAATCCAGAATCTAACCAAGCTGTAAGGTTGGTGCtt    <  2:376074/135‑1 (MQ=255)                                                                                                                                        aaTAACATTGAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAATATATGCGAAATTTGGTAAGGAGATTTATGTTGCAGCAAAATCTGGTGAACCCAATCCAGAATCTAACCCAGCTGTAAGGTTGGTGCTTGa  <  2:119176/140‑1 (MQ=255)                                                                                                                                        aaTAACATTGAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAATATATGCGAAATTTGGTAAGGAGATTTATGTTGCAGCAAAATCTGGTGAACCCAATCCAGAATCTAACCAAGCTTTAAGGTTGGTGCTTGa  <  1:458108/140‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                   ACAGTTTGAAGAAATCGTAGTTCAATAATGTTAATTGTGAAAATGTAT‑‑‑‑‑‑ATAAACATAAAAAAATCATGTATAATATATGTTGTTAATTAAACAGTTCGAAAGCGAGATGACATTATGGGACGTAAATGGAATAACATTAAAGAAAAAAAGGCCCAAAAAGATAAAAACACAAGTAGAATATATGCGAAATTTGGTAAGGAGATTTATGTTGCAGCAAAATCTGGTGAACCCAATCCAGAATCTAACCAAGCTTTAAGGTTGGTGCTTGA  >  CP000730/745590‑745858

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: ‑