Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000731	81	N→G	intergenic (–/‑151)	– / → repA	–/replication protein A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000731	81	0	N	G	95.9%	138.2 / NA	50	intergenic (–/‑151)	–/repA	–/replication protein A
Reads supporting (aligned to +/- strand):  ref base N (0/0);  major base G (29/18);  minor base A (0/2);  total (29/21)
Fisher's exact test for biased strand distribution p-value = 1.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTANAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAACTAAAATATGGAAAG  >  CP000731/1‑219                                                                                                                                          |                                                                                                                                           tatttatcaagggtttataaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGaa                                                                                                                                          >  1:14532‑M1/58‑140 (MQ=255)        caagggtttataaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTAttt                                                                                                                                   <  2:149243‑M1/90‑1 (MQ=255)                     acccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAAttt                                                                                                                      >  2:12991‑M1/38‑140 (MQ=255)                        cttgataaagctatattttcccttttataagtttGTTTAAATTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCg                                                                                                                   >  2:65872‑M1/35‑140 (MQ=255)                        cttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAAAAACTGTTTATTTATATAATTTTCg                                                                                                                   <  1:215940‑M1/106‑1 (MQ=255)                           gataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATa                                                                                                                >  1:55795‑M1/32‑140 (MQ=255)                                agctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATacttat                                                                                                           >  1:51446‑M1/27‑138 (MQ=255)                                agctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGt                                                                                                           >  1:39184‑M1/27‑140 (MQ=255)                                  ctatattttcccttttataagtttATTTAAAGTGCTATCATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGtat                                                                                                         >  1:125632‑M1/25‑140 (MQ=255)                                          tcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAAt                                                                                                 <  1:180471‑M1/124‑1 (MQ=255)                                           cccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATAATTGTATTATATAATg                                                                                                <  1:94710‑M1/125‑1 (MQ=255)                                                      gtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTAGATACTTGTATTATATAATGAATAATAACtt                                                                                     <  2:70364‑M1/136‑1 (MQ=255)                                                          aTTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTg                                                                                 <  1:175764/140‑1 (MQ=255)                                                              aaaGTGCTATAATAAATTTAATATAACAAAAACCCCAACTATTGCGAATAGTCGGGGTTTGGTAATAAAACGTTTAAAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAg                                                                             <  2:248320/140‑1 (MQ=255)                                                              aaaGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGCAACTGTTTATGTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAg                                                                             <  1:100741/140‑1 (MQ=255)                                                               aaGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAgt                                                                            >  2:262877/1‑139 (MQ=255)                                                                aGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAATCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCAATACTTTTATTATATAATAAATAATATTTTAATGCCAgaa                                                                           >  2:148520/1‑138 (MQ=255)                                                                aGTGCTATAATAAACTTAATATAACAAAAACCACAACTACTGGTAATAGTAGGGGTTTGGTAATAAAAAGTTTAGAAAATGTTTATTTATATAATTTTCGATATTTGTATTGTATAATGAATAATATTTTAGTGCAAGCa                                                                           >  2:150273/1‑140 (MQ=255)                                                                 gTGCTATAATAAACTTAATATAACAAAAACCCCCACTACTGGTAATACTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCAc                                                                          <  1:181774/140‑1 (MQ=255)                                                                  tGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATCATCGCCTTACCCAACGCCTCATATCTTAGTGCAAGCAcc                                                                         <  1:63442/140‑1 (MQ=255)                                                                  tGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCAcc                                                                         <  1:144050/140‑1 (MQ=255)                                                                          taaACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCAt                                                                 <  1:125061/140‑1 (MQ=255)                                                                             aCTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATAAATAATAACTTAGTGCAAGCACCTAAATCATtaa                                                              >  1:84999/1‑140 (MQ=255)                                                                                 aaTATAAAAAAAACGCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATtaaataa                                                          <  2:140513/140‑1 (MQ=255)                                                                                       aCAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTaa                                                    >  1:174454/1‑140 (MQ=255)                                                                                          aaacCCCCCACCACCGGTAATACGCGGGGTTTGGTAAAAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGc                                                 <  1:57894/140‑1 (MQ=255)                                                                                           aaaCCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCt                                                >  2:14365/1‑140 (MQ=255)                                                                                               cccAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCtaaat                                            >  2:181262/1‑140 (MQ=255)                                                                                               caaaaCTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCtaaat                                            <  2:61175/137‑1 (MQ=255)                                                                                                tcAACTACTGGTAATAGTTGGGGTTTGGTAATAAAACGTTTATAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAACGACTGATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCtaaata                                           <  2:187636/139‑1 (MQ=255)                                                                                                tcAAATACTGGTAATAGTCGGGGTTTGGTAATAAATCGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCtaaata                                           <  2:235345/139‑1 (MQ=255)                                                                                                 cAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATATATGTTAAGCtaaataa                                          >  1:98799/1‑140 (MQ=255)                                                                                                 cAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCtaaataa                                          >  1:20658/1‑140 (MQ=255)                                                                                                 cAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGAACCTAAATCATTAAATAAATGTAAAGCtaaataa                                          >  1:236720/1‑140 (MQ=255)                                                                                                         tgTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGttt                                  <  1:17329/139‑1 (MQ=255)                                                                                                         ggTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGACTAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGttt                                  >  1:65296/1‑140 (MQ=255)                                                                                                            aaTAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTttat                               >  1:172479/1‑140 (MQ=255)                                                                                                              tAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATATTAGAGAAAGCACCTAAATCATTAAATAAATATAATACTAAATAAAAACGCTtgatta                             >  2:160680/1‑140 (MQ=255)                                                                                                                gTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATCAcc                           >  2:138521/1‑140 (MQ=255)                                                                                                                   ggggTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACctct                        >  1:187963/1‑140 (MQ=255)                                                                                                                     ggTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTa                      >  2:134389/1‑140 (MQ=255)                                                                                                                      gTTTGGTAATAAAACGTTTAGATACTGTTTTGTTTTAGAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTAc                     >  1:194853/1‑140 (MQ=255)                                                                                                                      gTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACTTCTTAc                     >  1:174693/1‑140 (MQ=255)                                                                                                                       tttGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTAcc                    <  1:43723/140‑1 (MQ=255)                                                                                                                       tttGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATAATTAAATAAATGTAAAGCTAAATAAAAACGATTTATTACCTCTTAcc                    >  2:69247/1‑140 (MQ=255)                                                                                                                          ggTAATAGACCATTTAGAAACGGTTTATTTATATAATTTTAGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCaaa                 <  2:98849/140‑1 (MQ=255)                                                                                                                          ggTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCaaa                 >  1:215599/1‑140 (MQ=255)                                                                                                                                     gTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTCCATCTTACCAAACTAAAACATgg      >  2:166672/1‑140 (MQ=255)                                                                                                                                      tttAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAACTAAAATATGGa     >  1:182005/1‑140 (MQ=255)                                                                                                                                         aGAAACTGTTTATTTATATAATTTTCCATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAACTAAAATATGGAAag  <  2:41967/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                                           ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTANAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAACTAAAATATGGAAAG  >  CP000731/1‑219

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: ‑