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	96.8%	198.8 / NA	63	intergenic (–/‑151)	–/repA	–/replication protein A
Reads supporting (aligned to +/- strand):  ref base N (0/0);  major base G (35/25);  minor base A (0/2);  total (35/28)
Fisher's exact test for biased strand distribution p-value = 1.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTANAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAACTAAAATATGGAAA  >  CP000731/1‑218                                                                                                                                       |                                                                                                                                          ttatcaagggtttataaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATCAAACGTTTAGAAACt                                                                                                                                      <  1:91745‑M1/86‑1 (MQ=255) ttatcaagggtttataaacccttgataaagctatattttcacttttataagtttATTTAAAGTGCTATACTAAACTTAATATAACAAAAACACCAACTGCTGGTAATAGTCGGGGTTTGGTAATCAAACGATTAGAAACt                                                                                                                                      <  2:68111‑M1/86‑1 (MQ=255)     caatgttttataaacccttgataaagctatattttccattttataagtttATTTAAATTGCTATAATAAACTTAATATAACAAAAACCTCAACTACTGTTAATATTCTGGTTTTGCTAATAAAAAGCTTATAAACTGttt                                                                                                                                  <  2:1343‑M1/90‑1 (MQ=255)      aagggtttataatcccttgataaagctatattttcccttttataagtttATTTAAAGTGCGATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGttta                                                                                                                                 >  1:44050‑M1/50‑140 (MQ=255)       agggtttataaacccttgataaagctatattttcccttttataaggtaTGTTAAAGGGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGtttat                                                                                                                                <  1:154569‑M1/92‑1 (MQ=255)            ttataaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAATAGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTtata                                                                                                                           <  1:15524‑M1/97‑1 (MQ=255)             tataaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGATTAGAAACTGTTTATTtatat                                                                                                                          <  2:30488‑M1/98‑1 (MQ=255)              ataaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTtatata                                                                                                                         <  1:47585‑M1/99‑1 (MQ=255)               taaacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATaa                                                                                                                        <  2:80110‑M1/100‑1 (MQ=255)                 aacccttgataaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCAGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAAtt                                                                                                                      <  2:255129‑M1/102‑1 (MQ=255)                  actattgataaagttagaatttcccttttataagttaAGTGAAATTGCTATAATCAGCTTATGATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAAttt                                                                                                                     >  2:175071‑M1/38‑140 (MQ=255)                    tcttgataaaactatattttcccttttataatgttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAGCTACTTGTAACAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTc                                                                                                                   >  1:163467‑M1/36‑140 (MQ=255)                          taaaggtgtattgttcctgttatgagtttATGTAAAGTGCTATGATAAACTTAATATAACAAAAACCGCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACt                                                                                                             >  2:257434‑M1/30‑140 (MQ=255)                          taaagctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACt                                                                                                             >  1:83567‑M1/30‑140 (MQ=255)                             agctatattttcccttttataattttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGt                                                                                                          >  1:8082‑M1/27‑140 (MQ=255)                             agctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTTGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGt                                                                                                          >  2:137350‑M1/27‑140 (MQ=255)                             agctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGt                                                                                                          >  1:59113‑M1/27‑140 (MQ=255)                             agctatattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGt                                                                                                          <  2:165789‑M1/114‑1 (MQ=255)                                 atattttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGtatta                                                                                                      >  1:224630‑M1/23‑140 (MQ=255)                                     tttcccttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATtatata                                                                                                  >  2:183551‑M1/19‑140 (MQ=255)                                     tttcccgtttatcagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATtatata                                                                                                  >  2:135357‑M1/19‑140 (MQ=255)                                           ttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAATCCCCAATTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGaat                                                                                            >  2:25383‑M1/13‑140 (MQ=255)                                           ttttataagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGaat                                                                                            >  1:58767‑M1/13‑140 (MQ=255)                                             ttataagtttATTTAAAGTGGTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGaataa                                                                                          >  1:101454‑M1/11‑140 (MQ=255)                                                taagtttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAatat                                                                                       <  1:43610‑M1/133‑1 (MQ=255)                                                     ttATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAAATACTGGTAATAGTCGTGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAg                                                                                  >  2:263447‑M1/3‑140 (MQ=255)                                                         ttAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCa                                                                              >  1:54505/1‑140 (MQ=255)                                                           aaaGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAg                                                                            <  1:203373/140‑1 (MQ=255)                                                             aGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGATTATTTCTCTAATTTGCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCa                                                                          <  1:50958/140‑1 (MQ=255)                                                              gggCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTTGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCAc                                                                         <  2:5461/138‑1 (MQ=255)                                                               tGCTATAATAAGCTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATACAACGTTTAAAAAGTGTTTATTTATCTGGTGATCGATACTTGTATTATATAATTTATAATATCTTTGTGCAAGCAcc                                                                        <  2:57675/140‑1 (MQ=255)                                                               tGCTATAATAAACGTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCAcc                                                                        <  1:187906/140‑1 (MQ=255)                                                                 cTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTa                                                                      >  1:134301/1‑140 (MQ=255)                                                                   ataataAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTaaa                                                                    <  2:154569/140‑1 (MQ=255)                                                                      ataaACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCa                                                                 >  1:92913/1‑140 (MQ=255)                                                                       taaACTTAATATAACAAAAACCCCATCTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCAt                                                                <  1:68111/140‑1 (MQ=255)                                                                       taaACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCAt                                                                <  2:91745/140‑1 (MQ=255)                                                                        aaaCTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCAtt                                                               <  1:128907/140‑1 (MQ=255)                                                                                 ataACAAAAACCCCAACTACTGATAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATg                                                      <  2:99598/140‑1 (MQ=255)                                                                                  taACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAACACGTGTAAAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGt                                                     <  1:193668/140‑1 (MQ=255)                                                                                   aaCAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTa                                                    >  1:138172/1‑140 (MQ=255)                                                                                         aaCCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATATTTGTATTATATAATGAATAATATCTTAGTGCAAGCACATAAATCATTAAATAAATGTAAAGCta                                              >  1:23491/1‑140 (MQ=255)                                                                                         aaCCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCta                                              >  2:91560/1‑140 (MQ=255)                                                                                         aaCCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCta                                              >  1:36071/1‑140 (MQ=255)                                                                                         aaCCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAACta                                              >  1:93827/1‑140 (MQ=255)                                                                                          aCCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCtaa                                             <  1:56383/140‑1 (MQ=255)                                                                                           ccccAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTACATCCTACGCTACATGTAAAGCtaaa                                            >  1:35553/1‑140 (MQ=255)                                                                                            cccAACTACTGGTAATAGTCGGTGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCtaaat                                           <  2:139687/140‑1 (MQ=255)                                                                                               aaCTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTATAGCtatataaa                                        >  2:14620/1‑140 (MQ=255)                                                                                                 ctactGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATaaaaa                                      >  1:143175/1‑140 (MQ=255)                                                                                                 ctactGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTAGGGAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATaaaaa                                      >  1:74435/1‑140 (MQ=255)                                                                                                    ctGGTAATAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATTAATGTAAAGCTAACTAAAAACGt                                   >  1:172982/1‑140 (MQ=255)                                                                                                          aTAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTattatt                             >  2:37301/1‑140 (MQ=255)                                                                                                           tAGTCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTttatta                            <  1:56925/140‑1 (MQ=255)                                                                                                              ttggggTTTGGTAATAAAACGTTTAGTAACTGTTTATTTATATAATTTTAGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACct                         <  2:123837/138‑1 (MQ=255)                                                                                                              tCGGGGTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACct                         <  2:134301/140‑1 (MQ=255)                                                                                                                ggggTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACctct                       >  2:185482/1‑140 (MQ=255)                                                                                                                ggggTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACctct                       >  2:148629/1‑140 (MQ=255)                                                                                                                ggggTTTGGTAATAAAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATCACctct                       >  2:215278/1‑140 (MQ=255)                                                                                                                           ataaAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAACTaa            >  1:205135/1‑140 (MQ=255)                                                                                                                            taaAACGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAACTaaa           >  2:48054/1‑140 (MQ=255)                                                                                                                               aaCGTTTAGAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAACTAAAata        <  1:65593/140‑1 (MQ=255)                                                                                                                                     tAGAAACTGTTTATTTATATAATTTTAGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAACTAAAATATGGaaa  >  1:115682/1‑140 (MQ=255)                                                                                                                                       |                                                                                                                                          ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATTTAAAGTGCTATAATAAACTTAATATAACAAAAACCCCAACTACTGGTAATAGTCGGGGTTTGGTAATAAAACGTTTANAAACTGTTTATTTATATAATTTTCGATACTTGTATTATATAATGAATAATATCTTAGTGCAAGCACCTAAATCATTAAATAAATGTAAAGCTAAATAAAAACGTTTTATTACCTCTTACCAAACTAAAATATGGAAA  >  CP000731/1‑218

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: ‑