Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	188,740	C→G	I133M (ATC→ATG)	pyrH →	uridylate kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	188,740	0	C	G	90.0%	201.1 / 14.0	60	I133M (ATC→ATG)	pyrH	uridylate kinase
Reads supporting (aligned to +/- strand):  ref base C (3/3);  new base G (32/22);  total (35/25)
Fisher's exact test for biased strand distribution p-value = 6.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.12e-01

CCTGGCAATGCGTGATGCACTGCACCGCGCCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATCCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGAAAGCAACCAAAGTTGACGGCGTGTTTACCGCTGATCCGGCG  >  CP009273/188605‑188869                                                                                                                                        |                                                                                                                                  ccTGGCAATGCGTGATGCACTGCACCGCGCCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGct                                                                                                                                 >  1:528654/1‑138 (MQ=255)  cTGGCAATGCGTGATGCACTGCACCGCGCCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGctc                                                                                                                                <  1:2472134/138‑1 (MQ=255)      cAATGCGTGATGCACTGCACCGCGCCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTccg                                                                                                                            <  1:3845630/138‑1 (MQ=255)           cGTGATGCACTGCACCGCGCCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGt                                                                                                                       >  1:4188356/1‑138 (MQ=255)           cGTGATGCACTGCACCGCGCCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGt                                                                                                                       >  1:135695/1‑138 (MQ=255)            gTGATGCACTCCACCGCGCCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACACCTACAGCTGGGCAGAAGCTATCAGCCTGTTCCGCAACAACCGTTTGGTGATGCTCTCCGCCGGTa                                                                                                                      <  1:1908260/138‑1 (MQ=255)                   actgcacCGCGCCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAAc                                                                                                              <  1:874390/139‑1 (MQ=255)                   actgcacCGCGCCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAAc                                                                                                              <  1:241630/139‑1 (MQ=255)                    ctgcacCGCGCCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAAc                                                                                                              >  1:1067116/1‑138 (MQ=255)                     tgcacCGCGCCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAAccc                                                                                                            >  1:2686440/1‑139 (MQ=255)                            cgcCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCttt                                                                                                     >  1:3680655/1‑139 (MQ=255)                            cgcCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCttt                                                                                                     >  1:1635587/1‑139 (MQ=255)                            cgcCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGGAACCCGTTCttt                                                                                                     >  1:3609779/1‑139 (MQ=255)                                 aTGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGAAACAACCGTGTGTGGATGCTCTCCGCCGGTACAGGAAACCCGTTCTTTacca                                                                                                 >  1:98225/1‑138 (MQ=255)                                       aCGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACt                                                                                           >  1:4267928/1‑138 (MQ=255)                                                   tGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCt                                                                              <  1:3646777/139‑1 (MQ=255)                                                       cGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGCACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGt                                                                          >  1:2527798/1‑139 (MQ=255)                                                         cTATTCCATTGACTGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGtc                                                                                                                      >  1:238129/1‑92 (MQ=255)                                                         cTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTgg                                                                        >  1:1607750/1‑139 (MQ=255)                                                            ttCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTa                                                                      >  1:2377769/1‑138 (MQ=255)                                                            ttCCATTGAATGGCGTGTGCGAAAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTAt                                                                     <  1:3802393/139‑1 (MQ=255)                                                               cATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGACGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCg                                                                                                           <  1:4204283/98‑1 (MQ=255)                                                               cATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGa                                                                  >  1:1300934/1‑139 (MQ=255)                                                                 ttGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACACCCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATc                                                                    <  1:1865001/135‑1 (MQ=255)                                                                 ttGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGaaa                                                                >  1:618996/1‑139 (MQ=255)                                                                  tGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAAt                                                               <  1:1054018/139‑1 (MQ=255)                                                                   gAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATCCTCTCCGCCGGTACAGGTAACCCGTTCTTTaccac                                                                                                <  1:371055/105‑1 (MQ=255)                                                                     aTGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGa                                                            <  1:1438761/139‑1 (MQ=255)                                                                      tGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGCAATTGaa                                                           >  1:3490022/1‑139 (MQ=255)                                                                         cGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTacca                                                                                                 >  1:2034527/1‑98 (MQ=255)                                                                         cGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGcc                                                        >  1:2424642/1‑139 (MQ=255)                                                                         cGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGc                                                         <  1:3778438/138‑1 (MQ=255)                                                                           tgtgCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCCGCTTGCCTGCGTGGAATCGAAATTGatg                                                          >  1:4035154/1‑133 (MQ=255)                                                                             tgCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATCCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTcagca                                                                                      >  1:2543814/1‑105 (MQ=255)                                                                              gCGACCGCTACAGCTGGGCAGAAGCTACCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGAtg                                                    <  1:3806218/138‑1 (MQ=255)                                                                              gCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGAtgt                                                   <  1:3228099/139‑1 (MQ=255)                                                                               ctgcagctacagctGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGAGGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGAtg                                                    <  1:2476091/134‑1 (MQ=255)                                                                               cGACAGCTACAGCTGAGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGTTACAGGTAACCCGTTCTTTACCACCGACTCCGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGAtggg                                                  >  1:2152966/1‑137 (MQ=255)                                                                                gACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATCCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGAtg                                                    <  1:1333416/136‑1 (MQ=255)                                                                                     ctacagctGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCg                                                                           <  1:1574053/108‑1 (MQ=255)                                                                                       acagctGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGaa                                          >  1:781166/1‑139 (MQ=255)                                                                                         agctGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTaccac                                                                                                <  1:3525268/83‑1 (MQ=255)                                                                                          gctGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATCCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCATCTTGCCTGCGTGGTATCGAAATTGAAGCCGCTGTGGGGCTGaa                                          >  1:3504656/1‑136 (MQ=255)                                                                                            tGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGaaa                                         <  1:513856/135‑1 (MQ=255)                                                                                             gggCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGaa                                          >  1:303210/1‑133 (MQ=255)                                                                                              ggCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGa                                                            <  1:1967803/114‑1 (MQ=255)                                                                                              ggCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGAAAGCAAcc                                   >  1:2138957/1‑139 (MQ=255)                                                                                               gCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGaa                                                                 >  1:3744784/1‑108 (MQ=255)                                                                                               acAGAAGCTATCAGTCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTCCCACCGACTCATCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGAAAGCAAcc                                   <  1:4080939/137‑1 (MQ=255)                                                                                                   aaGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTcagca                                                                                      >  1:1354072/1‑83 (MQ=255)                                                                                                        aTCAGCCTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGAtgtg                                                  >  1:4137673/1‑114 (MQ=255)                                                                                                             ccTGTTGCGCAACAACCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGAAAGCAACCAAAGTTGACGGCgtg                    >  1:2534030/1‑139 (MQ=255)                                                                                                                    cgcAACAACCGTGTGGTGATCCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGAAAGCaa                                     <  1:1114195/115‑1 (MQ=255)                                                                                                                      caacaaCCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGAAAGCAACCAAAGTTGAc                          <  1:1968421/124‑1 (MQ=255)                                                                                                                       aacaacCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGAAAGCAACCAAAGTTGACGGCGTGTTTACCGCTg          >  1:1321760/1‑139 (MQ=255)                                                                                                                         caacCGTGTGGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGc                                                         <  1:888992/90‑1 (MQ=255)                                                                                                                              gtgtGGTGATCCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGAAAGCAACCAAAGTTGa                           >  1:3285852/1‑115 (MQ=255)                                                                                                                               tgtgGTGATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGAAAGCAACCAAAGTTGACGGCGTGTTTACCGCTGATCCGGCg  >  1:2838313/1‑139 (MQ=255)                                                                                                                                gtggtgATGCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGAAAGCAACCAAAGTTGACGGCGTGTTTa                >  1:4138290/1‑124 (MQ=255)                                                                                                                                   gtgATGCTCTCCGCCGGTACAGGGAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATgtggtg                                               >  1:3061004/1‑90 (MQ=255)                                                                                                                                        |                                                                                                                                  CCTGGCAATGCGTGATGCACTGCACCGCGCCTATGTGAACGCTCGTCTGATGTCCGCTATTCCATTGAATGGCGTGTGCGACAGCTACAGCTGGGCAGAAGCTATCAGCCTGTTGCGCAACAACCGTGTGGTGATCCTCTCCGCCGGTACAGGTAACCCGTTCTTTACCACCGACTCAGCAGCTTGCCTGCGTGGTATCGAAATTGAAGCCGATGTGGTGCTGAAAGCAACCAAAGTTGACGGCGTGTTTACCGCTGATCCGGCG  >  CP009273/188605‑188869

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑