Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,440,085	G→T	intergenic (‑45/+126)	cspA_2 ← / ← USA300TCH1516_01338	Cold shock protein CspA/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,440,085	0	G	T	100.0%	165.1 / NA	50	intergenic (‑45/+126)	cspA_2/USA300TCH1516_01338	Cold shock protein CspA/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (20/30);  total (20/30)

TTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTATTGGTA  >  USA300TCH1516_ALE/1439940‑1440227                                                                                                                                                  |                                                                                                                                               ttAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCC‑TTTTCAGCGTTAGACCATTTAACTGTACCTTGTTTCATCATCTGAAACCTCCCAACCTAAAATTCATTCAATTTGCTTATTCTCat                                                                                                                                             <  1:925345/148‑1 (MQ=255)     ttGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATAtt                                                                                                                                          <  1:930097/148‑1 (MQ=255)     ttGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATAtt                                                                                                                                          <  1:313640/148‑1 (MQ=255)     ttGCTGAAAAATGTACGAATACGTCATTTTCGCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATAtt                                                                                                                                          <  1:473941/148‑1 (MQ=255)          gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAACATTCATTTCGTATGCTTATTATCATATTACaaa                                                                                                                                     >  1:1167519/1‑148 (MQ=255)            aaaaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaaa                                                                                                                                   <  1:1098920/148‑1 (MQ=255)               aTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATa                                                                                                                                >  1:872323/1‑148 (MQ=255)                 gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACa                                                                                                                              <  1:11557/148‑1 (MQ=255)                           gTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGCAACCTCCAGGACTAAAATTAATCCAATATGCTGATTCTCTTATTAAACAAAATCAAAACAAATTTc                                                                                                                    >  1:259238/1‑148 (MQ=255)                           gTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTc                                                                                                                    >  1:489090/1‑148 (MQ=255)                           gTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTc                                                                                                                    >  1:488862/1‑148 (MQ=255)                            tCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCa                                                                                                                   >  1:1010345/1‑148 (MQ=255)                             cATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAc                                                                                                                  >  1:211242/1‑148 (MQ=255)                               ttttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTc                                                                                                                <  1:942974/148‑1 (MQ=255)                                 ttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaa                                                                                                              >  1:443067/1‑148 (MQ=255)                                  tctcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACGAAAAGTACATGCAAATTTCACTCaaa                                                                                                             <  1:690504/148‑1 (MQ=255)                                     ccTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAatat                                                                                                          <  1:632282/148‑1 (MQ=255)                                        tCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                                                                                                       <  1:937668/148‑1 (MQ=255)                                        tCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAAACTCCAAGACTAAAATTCATTCAATATTCTTATTCTCATATTACAAAGAATACATGCAAATTTCACTCAAGTATTCt                                                                                                       >  1:800743/1‑148 (MQ=255)                                          aaCTTCGATAAAGCCGCATCCTGTTTCAGCGTTAAACCGTTTTTCAGGACGATACAATCTGATGTGCAAGCTCGAAGACTAAAATTCATTCAATATGCTTATTCTCATAGTACAAAACATACATGCAAATTTGACTCAAATATTCttt                                                                                                     >  1:919966/1‑148 (MQ=255)                                               cGATAAAGCCGAATCCTTTTTCAGCGTTAAACCACTTAACTGTACCTTGTCTCATAATCTGAAACAACCAAGACTAAAATTCCTTCAACATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAat                                                                                                <  1:600846/148‑1 (MQ=255)                                                      gCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaat                                                                                         >  1:1170659/1‑148 (MQ=255)                                                         gAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataat                                                                                      >  1:807709/1‑148 (MQ=255)                                                          aaTCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTACTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatc                                                                                     <  1:410429/148‑1 (MQ=255)                                                                   tCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTa                                                                            <  1:1097886/148‑1 (MQ=255)                                                                          tAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGta                                                                     <  1:439650/148‑1 (MQ=255)                                                                          tAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGta                                                                     <  1:717844/148‑1 (MQ=255)                                                                          tAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGta                                                                     <  1:638592/148‑1 (MQ=255)                                                                             aCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtatta                                                                  <  1:1029692/148‑1 (MQ=255)                                                                                     aCTGTACCTTGTTTCATACACTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAg                                                          <  1:903008/148‑1 (MQ=255)                                                                                     aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATTCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAg                                                          <  1:287476/148‑1 (MQ=255)                                                                                     aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAACTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAg                                                          <  1:448463/148‑1 (MQ=255)                                                                                          aCCTTGTTTCAAAATCTGAAACCTCCAAGACTAAAATTCATTAAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATACTTGTCCGTTTAACTTGTATTATAGTGCAGttatt                                                     <  1:925476/148‑1 (MQ=255)                                                                                                  tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAtt                                             <  1:506291/148‑1 (MQ=255)                                                                                                  tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAtt                                             <  1:820248/148‑1 (MQ=255)                                                                                                  tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAAAATTAGTGACAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAtt                                             >  1:1236250/1‑148 (MQ=255)                                                                                                            aaaacaccAAGACTAAAATTCATTCAATATGCTTATTCTCATCTTAATTAGAGTGCAGTCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAACTGcaatacaat                                   <  1:855612/142‑1 (MQ=255)                                                                                                            aaaCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACCAGTTAGTCATGCAAATTTCACTCAAAGATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAACTGcaatacaat                                   <  1:855471/148‑1 (MQ=255)                                                                                                            aaaCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatacaat                                   <  1:1210136/148‑1 (MQ=255)                                                                                                                  ccAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaa                             >  1:471965/1‑148 (MQ=255)                                                                                                                         tAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAACTATTCTTTGCAAAATGGAATAATCATCTGCTTAACTTGTATTATAGAGCAGCTATTACCAAATTGCAATACAATAATAAAAAAAAtt                      >  1:152735/1‑148 (MQ=255)                                                                                                                         tAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATAtt                      >  1:152631/1‑148 (MQ=255)                                                                                                                           aaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACGATAATAAAAACTATTcc                    >  1:827947/1‑147 (MQ=255)                                                                                                                           aaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCa                    <  1:1262150/148‑1 (MQ=255)                                                                                                                           aaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCa                    <  1:1068801/148‑1 (MQ=255)                                                                                                                                     aaTATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAat          >  1:509068/1‑148 (MQ=255)                                                                                                                                     aaTATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAat          >  1:937122/1‑148 (MQ=255)                                                                                                                                         tGCTTATTCTCATATGACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAattatt      <  1:837119/148‑1 (MQ=255)                                                                                                                                          gCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTATTg     <  1:306638/148‑1 (MQ=255)                                                                                                                                             tATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTATTGGTa  >  1:310939/1‑148 (MQ=255)                                                                                                                                                  |                                                                                                                                               TTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTATTGGTA  >  USA300TCH1516_ALE/1439940‑1440227

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑