Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,934,780	A→T	11.9%	N156K (AAT→AAA)	USA300HOU_RS09605 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,934,780	0	A	T	11.9%	127.1 / 10.1	42	N156K (AAT→AAA)	USA300HOU_RS09605	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (19/18);  new base T (3/2);  total (22/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.51e-01

AAAAATATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATAATTTT  >  USA300TCH1516_ALE/1934642‑1934917                                                                                                                                           |                                                                                                                                          aaaaaTATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAAtt                                                                                                                                         >  1:94310/1‑141 (MQ=255)  aaaaTATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTc                                                                                                                                        >  1:138762/1‑141 (MQ=255)    aaTATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGTAATTTaa                                                                                                                                      >  1:538255/1‑141 (MQ=255)       ataAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTATTTGAATTTCaaaaa                                                                                                                                   <  1:57076/141‑3 (MQ=255)        taAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCaaataa                                                                                                                                  <  2:184189/141‑1 (MQ=255)          aGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCaaataaat                                                                                                                                <  1:105735/141‑1 (MQ=255)          aGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCaaataaat                                                                                                                                >  2:307929/1‑141 (MQ=255)              tCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTATTTGAATTTCAAAAAAATATTc                                                                                                                            <  1:436983/141‑1 (MQ=255)                 atatTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAAGATTCttt                                                                                                                         <  1:510698/141‑1 (MQ=255)                    ttAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCg                                                                                                                      <  1:258931/141‑1 (MQ=255)                      aaTTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTa                                                                                                                    <  2:327046/141‑1 (MQ=255)                          tCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTAtttt                                                                                                                <  2:203891/141‑1 (MQ=255)                                      tCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCATACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAAAGAATATTTTTTTGAAATTCAAATATATATTTTTTGCGTATTTTGATTTCATCttt                                                                                                    >  1:351686/1‑140 (MQ=255)                                        aTAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATc                                                                                                  <  1:256895/141‑1 (MQ=255)                                             tttCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTaaaa                                                                                             >  1:205093/1‑141 (MQ=255)                                                  cTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCa                                                                                        >  1:329940/1‑141 (MQ=255)                                                     aaGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCAttt                                                                                     <  1:778463/141‑1 (MQ=255)                                                      aGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGAAAGTTACACACGAGATAGTGTTTAGTAGAAATGCTAATAAATTGGCTGTGCGTATTTTGAGTTCATCTTATCTAAAATATCAtttt                                                                                    >  2:114104/1‑141 (MQ=255)                                                      aGTATTTTTTCTTTTCTTCAAACTCTTCATCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCAtttt                                                                                    <  1:87217/141‑1 (MQ=255)                                                       gTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTc                                                                                   <  1:240679/141‑1 (MQ=255)                                                                    tcttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAGATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCtttt                                                                      <  1:198341/141‑1 (MQ=255)                                                                     cttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTa                                                                     >  1:227349/1‑141 (MQ=255)                                                                      ttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTaa                                                                    >  1:648590/1‑141 (MQ=255)                                                                      ttcAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTaa                                                                    >  1:256126/1‑141 (MQ=255)                                                                         aaaCTCTTCTTTCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTc                                                                 <  1:38418/141‑1 (MQ=255)                                                                               ttcttcCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAg                                                           >  1:502394/1‑141 (MQ=255)                                                                                   tcCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGatat                                                       <  2:175950/141‑1 (MQ=255)                                                                                        ttCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAat                                                  >  1:229874/1‑141 (MQ=255)                                                                                        ttCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTCTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAat                                                  <  1:620967/141‑1 (MQ=255)                                                                                                     ttGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTa                                     >  1:57332/1‑141 (MQ=255)                                                                                                                 tCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTa                         >  1:57152/1‑141 (MQ=255)                                                                                                                 tCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTa                         >  2:9653/1‑141 (MQ=255)                                                                                                                  cTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTaa                        <  1:358663/141‑1 (MQ=255)                                                                                                                     aaTTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAg                     >  2:132108/1‑141 (MQ=255)                                                                                                                      cgcaaagaATATTTATTTGAATTTCAAAAAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGa                    >  2:239931/6‑141 (MQ=39)                                                                                                                       ttAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGaa                   >  2:119657/1‑141 (MQ=255)                                                                                                                             aaTATTTATTTGAATTTCAAAAAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCt             >  1:448999/1‑141 (MQ=255)                                                                                                                                  ttatttGAATTTCAAAAAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCtat        >  1:399621/4‑141 (MQ=255)                                                                                                                                    ttttGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATaa      <  1:702976/141‑1 (MQ=255)                                                                                                                                       tGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATAAttt   <  2:322881/141‑1 (MQ=255)                                                                                                                                        gAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATAAtttt  >  1:389596/1‑141 (MQ=255)                                                                                                                                        gAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATAAtttt  <  1:4896/141‑1 (MQ=255)                                                                                                                                           |                                                                                                                                          AAAAATATAAGGGTCAATATTAATTTCGTCTATCAATTCATAAATTTCACTTAAGTATTTTTTCTTTTCTTCAAACTCTTCTTCCAGTTCCAAATAATTATTGACTGATTGTTCTAAATTAGAGAATATTTTTTTGAAATTCAAATAAATATTCTTTGCGTATTTTGATTTCATCTTATCTAAAATATCATTTTCGATATAACCTTTTAATTCTTTTAGATATGAAATATTAGTATATTTAAAATTATTGGTAATAGAAATACCTTCTATAATTTT  >  USA300TCH1516_ALE/1934642‑1934917

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑