Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,589,223	A→G	7.7%	V753V (GTT→GTC)	USA300HOU_RS07800 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,589,223	0	A	G	7.7%	145.6 / 4.2	52	V753V (GTT→GTC)	USA300HOU_RS07800	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (39/9);  new base G (2/2);  total (41/11)
Fisher's exact test for biased strand distribution p-value = 1.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.79e-01

ATAATCTTTTCCAAATCGAATTTTCCCACTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCTAGGAATTGGTGTGTT  >  USA300TCH1516_ALE/1589085‑1589363                                                                                                                                           |                                                                                                                                               aTAATCTTTTCCAAATCGAATTTTCCCACTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTcaac                                                                                                                                              <  2:221012/141‑1 (MQ=255)               aTCGAATTTTCCCACTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCAATAGATCCTCTACTATCTCCCTTATCTTTACCAAACCATTCAACAAACACTTCacacc                                                                                                                                >  2:620846/1‑137 (MQ=255)                    aTTTTCCCACTTTTATTACCATCATATACAGCCCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCGCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAg                                                                                                                           <  2:66299/141‑1 (MQ=255)                       ttCCCACTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGAcc                                                                                                                        >  1:937502/1‑141 (MQ=255)                            aCTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCGACAAACACTTCAAGCGCACAGACCTTAtt                                                                                                                   >  2:245245/1‑141 (MQ=255)                            aCTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCGACAAACACTTCAAGCGCACAGACCTTAtt                                                                                                                   >  2:913130/1‑141 (MQ=255)                                   ttaCCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCa                                                                                                            >  2:593624/1‑141 (MQ=255)                                   ttaCCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCa                                                                                                            >  1:283684/1‑141 (MQ=255)                                   ttaCCATCATATACAAACCCAATTTCTAATTGTCTTAAGATGTTGGAAACCTTTCTAATTTCCATAGAACCTCTACGATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCa                                                                                                            >  2:593671/1‑141 (MQ=255)                                       ctttttatgCAGACCAATTGTCTAATTTTCTTAGGATGTTTGAAGTCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCATAACATTCAACAAACACTTCCAGCGCACCCACCTTATTTCTTTTAACgg                                                                                                        <  2:157064/136‑2 (MQ=255)                                           atatACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAACGCACAGCCCTTATTTCTTTCAACGTAATc                                                                                                    >  1:28726/1‑141 (MQ=255)                                            tataCAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCt                                                                                                   <  2:248430/141‑1 (MQ=255)                                              taCAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTAc                                                                                                 >  1:644850/1‑141 (MQ=255)                                                 aGACCCATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCCCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAt‑t                                                                                             <  1:398574/141‑1 (MQ=255)                                                      aattgtctaattgtctTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTg                                                                                        <  1:514682/141‑1 (MQ=255)                                                       attgtctaattgtctTAAGACGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTGCTTTCAACGTAATCTACAT‑TTCCTGt                                                                                       >  1:572975/1‑141 (MQ=255)                                                         tttctaatggtctTAAAATGTTTGAAATCTTTCTGATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACAGTTCACGAGAAACTGGATTAGTTCTTTCAACGTACTCTACAT‑TTCCTGtat                                                                                     >  2:661574/3‑139 (MQ=255)                                                          gtctaattgtctTAAGTTGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTAGCTCCCTTATCTTTACGAAAACATTCAACAAACACTTCAGGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTgg                                                                                    >  1:467876/1‑141 (MQ=255)                                                          gtctaattgtctTAAGCTGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTgg                                                                                    >  1:561023/1‑141 (MQ=255)                                                            ctaattgtctTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCACCGTCATCTACAT‑TTCCTTTTGGTa                                                                                  >  1:120603/1‑141 (MQ=255)                                                                     ttAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTCCAT‑TTCCTGTCGGTAACATATCac                                                                         >  2:29615/1‑140 (MQ=255)                                                                     ttAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCaa                                                                         >  2:29645/1‑141 (MQ=255)                                                                      tAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAAc                                                                        >  1:248897/1‑141 (MQ=255)                                                                        aGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACAATTCAACaa                                                                      >  2:315094/1‑140 (MQ=255)                                                                           tGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCAc                                                                   >  2:268104/1‑141 (MQ=255)                                                                                gAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTgt                                                              >  1:249726/1‑140 (MQ=255)                                                                                      tttCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACACCACCTTGATAAAAt                                                        >  1:142510/1‑141 (MQ=255)                                                                                         cTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGt                                                    >  1:190771/1‑141 (MQ=255)                                                                                          tAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTc                                                   >  1:733495/1‑141 (MQ=255)                                                                                                ccATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGtt                                             >  1:734679/1‑141 (MQ=255)                                                                                                    aGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCGACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCaaa                                         <  1:913130/141‑1 (MQ=255)                                                                                                    aGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCGACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCaaa                                         <  1:245245/141‑1 (MQ=255)                                                                                                    aGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCaaa                                         >  1:393639/1‑141 (MQ=255)                                                                                                    aGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAAAATCCCGTCAGTAAAAT‑CGTCTTCGttataa                                         >  1:401087/1‑137 (MQ=255)                                                                                                     gATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAg                                        >  1:131676/1‑141 (MQ=255)                                                                                                            tactaTCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTa                                 >  2:814176/1‑141 (MQ=255)                                                                                                              ctaTCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTAAg                               >  1:738960/1‑141 (MQ=255)                                                                                                              ctaTCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTAAg                               >  1:374774/1‑141 (MQ=255)                                                                                                               taTCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTAAGt                              >  1:143302/1‑141 (MQ=255)                                                                                                                  ctcCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATAATAACCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTAAGTCAt                           >  1:880814/1‑141 (MQ=255)                                                                                                                   tcCCTTATCTGTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTGGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCATAGATAGTTAAGTCATc                          >  2:319999/1‑141 (MQ=255)                                                                                                                    cccTTATCTTTACCAGAACATTCAACGAACACTTTAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGTTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTCCAAAGATAGTTAAGTCATcc                         <  1:571909/141‑1 (MQ=255)                                                                                                                    cccTTATCTTTACCAAAACATTCAACAAACACTTCCAGCACACAGCCCTTATTTCTTTCAACGTACACTTAATCTTCCT‑TTCATGACATCTCAACATTGCCATG‑TAAAATGCGTCTTCGTTCAAAGATAGTTAAGTCATcc                         >  2:452596/1‑141 (MQ=255)                                                                                                                    cccTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTAAGTCATcc                         <  2:795851/141‑1 (MQ=255)                                                                                                                       ttATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCGACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTAAGTCATCCCaa                      >  1:512509/1‑141 (MQ=255)                                                                                                                        tATCTTTACCAAAACATTCAACAAACACTTCAAGCGCAAAGACCTTATTTCTTTCCACGTAATCTACAT‑TTCCTGTTGGTAACCTATAAACATCCCTTTCATATAAA‑TTTACTCGTTCAGAGGGAGTCAAGTCATCCCCAt                     >  2:890358/1‑141 (MQ=255)                                                                                                                          tCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTGCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACAGCACCTTTATAAAAG‑CGTCTTCGTTCAAGGATAGTTAAGTAATCCCAATTg                   >  1:38793/1‑141 (MQ=255)                                                                                                                            tttACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCt                 >  2:588974/1‑141 (MQ=255)                                                                                                                               aCCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCTAgg              <  2:733495/141‑1 (MQ=255)                                                                                                                               aCCAAAACATTCAACAAACACTTCAAGCGCACACACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGACAGTTAAGTCATCCCAATTGCTAgg              <  1:604109/141‑1 (MQ=255)                                                                                                                                  aaaaCATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAAATAGTTAAGTCATCCCAATTGACAGGAAt           >  2:347842/1‑141 (MQ=255)                                                                                                                                   aaaCATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCTAGGAAtt          >  2:490100/1‑141 (MQ=255)                                                                                                                                         tCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATACCCTTGCTAAAAT‑CGTCTGCGTTCAAAGACAGTTAAGTAATCCCAATGGCTGGGATTAGgtgtg    >  2:803617/1‑141 (MQ=255)                                                                                                                                          caaaaaACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCTAGGAATTGgtgtgt   >  2:299830/1‑141 (MQ=255)                                                                                                                                           aacaaacaCTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCTAGGAATTGGTGTGtt  >  2:893448/1‑141 (MQ=255)                                                                                                                                           aacaaacaCTTCAAGAACACAGACCTCTGTTCTTTCAACGTAATCTACAT‑TTCCTGCCGGTCACATATCAACATCACCTTGGACAAAT‑GACCTTCGTCCAACGAAAGTACAGTCATCCAACTGGCTAGGAATTgacgagag  >  2:913752/1‑134 (MQ=255)                                                                                                                                           |                                                                                                                                               ATAATCTTTTCCAAATCGAATTTTCCCACTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAT‑TTCCTGTTGGTAACATATCAACATCACCTTGATAAAAT‑CGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCTAGGAATTGGTGTGTT  >  USA300TCH1516_ALE/1589085‑1589363

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: ‑