Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,778,338	C→A	12.6%	*314Y (TAG→TAT)	arcC2 ←	Carbamate kinase 2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,778,338	0	C	A	12.6%	115.1 / 9.6	48	*314Y (TAG→TAT)	arcC2	Carbamate kinase 2
Reads supporting (aligned to +/- strand):  ref base C (21/20);  new base A (3/3);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.95e-01

CTAATTTATTATTTCTACCCAAAATAAAGTTTTCTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTCAACAAATCGTATCGCAGCTTCTATTTTTGGCAACATCGATCCTTCCA  >  USA300TCH1516_ALE/2778200‑2778477                                                                                                                                           |                                                                                                                                            cTAATTTATTATTTCTACCCAAAATAAAGTTTTCTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTa                                                                                                                                           >  2:302432/1‑141 (MQ=255)  tAATTTATTATTTCTACCCAAAATAAAGTTTTCTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTAc                                                                                                                                          >  1:70130/1‑141 (MQ=255)  tAATTTATTATTTCTACCCAAAATAAAGTTTTCTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTAc                                                                                                                                          >  2:121480/1‑141 (MQ=255)       tattatTTCCACCCAAGATAAAGTTTTCTGTCATAAGTTAAACTCCTTCACACCTTGCGAAGTGTAAGCAGACAACTTTTCCATTTGAATCATCGGAGAAACATATTTAATGGTTTGTCGCCTGATAAAGTGCTACAtgtg                                                                                                                                     <  2:134488/141‑1 (MQ=255)         ttattTCTACCCAAAATAAAGTTTTCTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGaa                                                                                                                                   >  2:360168/1‑141 (MQ=255)           attTCTACCCAAAATAAAGTTTTCTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAAtg                                                                                                                                 >  1:298712/1‑141 (MQ=255)                    cAAAATAAAGTTTTCTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTAAATGTGTGTACCt                                                                                                                        >  2:285366/1‑141 (MQ=255)                     aaaaTAAAGTTTTCTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAATGCTACATGTAAATGTGTGTACCtt                                                                                                                       >  2:208794/1‑141 (MQ=255)                             gTTTTCTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTAATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCa                                                                                                               >  1:378102/1‑141 (MQ=255)                              ttttCTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGATACATGTGAATGTGTGTACCTTTATTACCaa                                                                                                              >  2:43481/1‑141 (MQ=255)                              ttttCTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGATACATGTGAATGTGTGTACCTTTATTACCaa                                                                                                              >  2:357753/1‑141 (MQ=255)                              ttttCTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGATACATGTGAATGTGTGTACCTTTATTACCaa                                                                                                              >  2:43468/1‑141 (MQ=255)                                  cTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCaa                                                                                                          >  1:16642/1‑141 (MQ=255)                                       aTAAGTTAACCTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCtt                                                                                                     <  1:144238/141‑1 (MQ=255)                                       aTAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCtt                                                                                                     <  1:381483/141‑1 (MQ=255)                                            ttAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTAt                                                                                                <  2:298712/141‑1 (MQ=255)                                             tAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTTTTTTTTTTTTACGGAGAAACATATTTAATGTTTTATCGCGTGATACAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATg                                                                                               >  2:393175/1‑141 (MQ=255)                                              aaaCTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGc                                                                                              >  2:220844/1‑141 (MQ=255)                                                    cTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTAGATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGctc                                                                                        <  1:261893/141‑1 (MQ=255)                                                     ttCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGctct                                                                                       >  2:106610/1‑141 (MQ=255)                                                        aaaCCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTaaa                                                                                    >  1:178378/1‑141 (MQ=255)                                                        aaaCCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTCGTCTaaa                                                                                    >  1:158120/1‑141 (MQ=255)                                                           ccTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTg                                                                                 >  2:50386/1‑141 (MQ=255)                                                                 aaaGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATg                                                                           >  2:326311/1‑141 (MQ=255)                                                                 aaaGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATg                                                                           >  2:307271/1‑141 (MQ=255)                                                                  aaGTGTCATGAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTACTGTTTTGTCGTGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGa                                                                          <  2:287533/141‑1 (MQ=255)                                                                  aaGTGTCAGCAGACAACTTTTTCATTTGAATCAGCGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGa                                                                          <  2:232811/141‑1 (MQ=255)                                                                  aaGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTGTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGa                                                                          <  1:59227/141‑1 (MQ=255)                                                                  aaGGGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGa                                                                          <  1:299945/141‑1 (MQ=255)                                                                            agACAACTTTTTTTTTTTTTTTAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCTTTCTCTATATTTGTAATGATAACtttttt                                                                >  2:219844/1‑141 (MQ=255)                                                                                aaCTTGTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGGGAAAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGttt                                                            <  2:25719/141‑1 (MQ=255)                                                                                    ttttCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTccc                                                        <  1:245215/141‑1 (MQ=255)                                                                                          tttGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGATACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACttt                                                  <  1:357753/141‑1 (MQ=255)                                                                                          tttGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGATACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACttt                                                  <  1:43468/141‑1 (MQ=255)                                                                                          tttGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGATACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACttt                                                  <  1:43481/141‑1 (MQ=255)                                                                                           ttGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAAGCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTc                                                 <  2:161183/141‑1 (MQ=255)                                                                                            tGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTca                                                >  2:268570/1‑141 (MQ=255)                                                                                                  aaCGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTCAACAAAt                                          <  1:360168/141‑1 (MQ=255)                                                                                                      gagaAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTCAACAAATCGTa                                      <  1:212378/141‑1 (MQ=255)                                                                                                                tttCATGCTGTGTCGCGTGGTAAATTCCTACATGTGAATGTGTGTACCTTTGTGTCCAATCAAATCTTCGTTTGCCTTCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCTCCCTTTCAACAATTCGGATAGcgtcgtt                            <  2:47313/141‑7 (MQ=255)                                                                                                                tttAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTCAACAAATCGTATCGCAGCTTc                            <  1:121480/141‑1 (MQ=255)                                                                                                                             cgcgTGATAAAGTGTTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTCAACAAATCGTATCGCAGCTTCTATTTTTGGCAAc               >  1:140607/1‑141 (MQ=255)                                                                                                                               cgTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTCAACAAATCGTATCGCAGCTTCTATTTTTGGCAACAt             >  1:256635/1‑141 (MQ=255)                                                                                                                                gTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTCAACAAATCGTATCGCAGCTTCTCTTTTTGGCACCATc            >  2:336300/1‑141 (MQ=255)                                                                                                                                     aaaGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTCAACAAATCGTATCGCAGCTTCTATTTTTGGCAACATCGATcc       <  1:220844/141‑1 (MQ=255)                                                                                                                                     aaaGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTCAACAAATCGTATCGCAGCTTCTATTTTTGGCAACATCGATcc       <  1:49234/141‑1 (MQ=255)                                                                                                                                      aaGTGCCACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTCAACAAATCGTATCGCAGCTTCTATTTTTGGCAACATCGATCCt      <  2:21772/141‑1 (MQ=255)                                                                                                                                          gCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTCAACAAATCGTATCGCAGCTTCTATTTTTGGCAACATCGATCCTTCca  <  1:207563/141‑1 (MQ=255)                                                                                                                                           |                                                                                                                                            CTAATTTATTATTTCTACCCAAAATAAAGTTTTCTGTCATAAGTTAAACTCCTTCAAACCTTGCAAAGTGTCAGCAGACAACTTTTTCATTTGAATCAACGGAGAAACATATTTAATGTTTTGTCGCGTGATAAAGTGCTACATGTGAATGTGTGTACCTTTATTACCAATCAAAGCTTCGTATGCCTGCTCTAAATTGGTAATGATAACTTTTTTGTTTTCCCCACTTTCAACAAATCGTATCGCAGCTTCTATTTTTGGCAACATCGATCCTTCCA  >  USA300TCH1516_ALE/2778200‑2778477

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: ‑