Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,273,080	C→T	12.0%	intergenic (+45/+246)	PP_2003 → / ← PP_2004	hypothetical protein/AraC family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,273,080	0	C	T	12.0%	128.5 / 8.1	52	intergenic (+45/+246)	PP_2003/PP_2004	hypothetical protein/AraC family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (22/23);  new base T (3/3);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.13e-01

ACAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGATACCTACAAAGGCAAAATGAGCAAA  >  NC_002947/2272935‑2273228                                                                                                                                                  |                                                                                                                                                      aCAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGGCCCTTTCGCGGGCTGCCGGCGAAAGGGTCg                                                                                                                                                     <  6:248963/148‑1 (MQ=39) aCAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCg                                                                                                                                                     <  6:301691/148‑1 (MQ=255) aCAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTAGCCTGAACCGGCCCTTTCGCGGGCTGCCGGCGAAAGGGTCg                                                                                                                                                     <  3:67483/148‑1 (MQ=38)  cAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGt                                                                                                                                                   <  7:147925/149‑1 (MQ=255)   aGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGtt                                                                                                                                                  <  7:129729/149‑1 (MQ=255)     ccAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCa                                                                                                                                                <  7:1066/149‑1 (MQ=255)          gTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTg                                                                                                                                           >  8:59202/1‑149 (MQ=255)               cAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAAc                                                                                                                                      <  5:128421/149‑1 (MQ=255)                     gtgGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCCACCCATTCGCCGGCCGCCACCGAAATGGCCAGTTAAGGCTGAAAACAAccc                                                                                                                                 >  6:147971/1‑148 (MQ=255)                            cgccgGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACa                                                                                                                         <  2:236058/149‑1 (MQ=255)                            cgccgGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCGCCCTTTGATGGGTCGCCTGAACCCCCCCTTTCGCCGGCCGCCCGCGAAAGGGCCCGGTCACGCTGTAAACCTccccgggta                                                                                                                           >  5:152831/1‑142 (MQ=255)                               cggccgAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGAc                                                                                                                      <  7:239678/149‑1 (MQ=255)                                            aCCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAAc                                                                                                        >  5:111292/1‑149 (MQ=255)                                             cccATTCCGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTAGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCAGTAAACATCCCCTGTTACAGACGCCCCGCG‑AAAACt                                                                                                       >  2:84496/1‑149 (MQ=255)                                                aTTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTc                                                                                                    <  7:29679/149‑1 (MQ=255)                                                aTTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCAGAACCCACCCTTTCGCCGGCAGCCCGCCAAAGGGCCGGTTCAGGCTGTAAAAAACCCCAGTTAAAGACGCCCCGCC‑AATACttta                                                                                                    >  4:227614/1‑148 (MQ=255)                                                 ttCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCt                                                                                                   <  3:227614/149‑1 (MQ=255)                                                        gcagcaGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCGTTCGCCGGCAGCCCGCGAAAGGGGCGGGTCAGGCTGTTAACATACCCGGTTTCAGACGCCCCGCG‑ATAACTTTTTGCAAAcc                                                                                            >  7:121902/1‑149 (MQ=255)                                                              ggATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTAc                                                                                      <  7:59202/149‑1 (MQ=255)                                                                aTGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTAGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATACCCTGTTACAGACGCCCCGCG‑ATAACTTTCTg                                                                                                  >  8:172404/1‑135 (MQ=255)                                                                    ccAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCAGAACCGACCCATTAGCCGGCCGCCCGCGAAACGGCCGGTTAAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCAGAACCCCTGGAACGTTTaa                                                                                >  6:138164/1‑148 (MQ=255)                                                                     cAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGCAAGGGCCGGTTCAGGCTGGAAACATCCCCTGTTACAGCCGCCCCGCG‑ATAACTTTGTGAACACCTGCTACGTTTAc                                                                                >  5:264650/1‑148 (MQ=255)                                                                                  ccgccgccCCCTCCATTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCTAAAGGGCCGGTTCAGGCTGAAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCtt                                                                   <  5:147971/148‑1 (MQ=255)                                                                                   cgccgccCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGt                                                                 >  5:72372/1‑149 (MQ=255)                                                                                    gccgccCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGt                                                                 >  6:168447/1‑148 (MQ=255)                                                                                    gccgccCCCTCCCTTTGATGGGTCGCCGGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGtc                                                                <  6:152831/149‑1 (MQ=255)                                                                                        cccccTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGtcatca                                                            <  5:168447/149‑1 (MQ=255)                                                                                          ccctccctTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGCCGCCCCGCG‑ATAACGTTCTGCACACCTGGTACGTTTACCACTGAGAAGCTTGGCataatc                                                          >  7:143160/1‑149 (MQ=255)                                                                                          ccctccctTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGCATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTcatcat                                                           <  1:84496/149‑1 (MQ=255)                                                                                           cctccctTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCGGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATcc                                                         >  7:163675/1‑149 (MQ=255)                                                                                            ctccctTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCAt                                                                         <  2:234147/132‑1 (MQ=255)                                                                                                     aTGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCcg                                                                                                                <  3:79745/85‑1 (MQ=255)                                                                                                        ggTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCTGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCt                                            <  8:163675/149‑1 (MQ=255)                                                                                                         gTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTg                                           <  6:72372/149‑1 (MQ=255)                                                                                                          tCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCt                                                       <  8:137647/136‑1 (MQ=255)                                                                                                          tCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCt                                                       >  7:137647/1‑136 (MQ=255)                                                                                                             ccTGAACCGGCCCTTTCGCGGGCTGCCGGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCt                                         >  4:164544/1‑147 (MQ=255)                                                                                                              cTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGTCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACCCCTGCTACGTTTACCAGTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAg                                      >  3:275780/1‑149 (MQ=255)                                                                                                                       cccTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGtc                                                                >  8:121816/1‑114 (MQ=255)                                                                                                                       cccTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGtc                                                                <  7:121816/114‑1 (MQ=255)                                                                                                                        ccTTTCGCGGGCTGCCGGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACCCCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGc                             >  6:247900/1‑148 (MQ=255)                                                                                                                        ccTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGc                                                                     >  6:30245/1‑108 (MQ=255)                                                                                                                        ccTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGc                                                                     <  5:30245/108‑1 (MQ=255)                                                                                                                         cTTTCGCGGGCTGCCGGCGAAAGGGTCGGTTCAGCCAGTAAACATCCCATGTTACAGACGCCACGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCAATCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCg                            >  6:53286/1‑148 (MQ=255)                                                                                                                         cTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGa                           >  3:80901/1‑149 (MQ=255)                                                                                                                          tttCGCGGGCTGCCGGCGAAAGGGTCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAg                                      >  4:228163/1‑137 (MQ=255)                                                                                                                          tttCGCGGGCTGCCGGCGAAAGGGTCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAg                                      <  3:228163/137‑1 (MQ=255)                                                                                                                                     gCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGATACCTACAAAgg               >  5:247304/1‑149 (MQ=255)                                                                                                                                        cgcgAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGATACCTACaaa                 >  7:180531/1‑144 (MQ=255)                                                                                                                                        cgcgAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGATACCTACaaa                 <  8:180531/144‑1 (MQ=255)                                                                                                                                          cgAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGATACCTACAAAGGCaaa           >  6:42832/1‑148 (MQ=255)                                                                                                                                                ggCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGATACCTACAAAGGCAAAATGAGCa    <  6:247304/149‑1 (MQ=255)                                                                                                                                                  ccGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGATACCTACAAAGGCAAAATGAGCaaa  <  5:138164/149‑1 (MQ=255)                                                                                                                                                  ccGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGATACCTACAAAGGCAAAATGAGCaaa  <  6:111292/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                      ACAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCCGAGGCCGCCGCCCCCTCCCTTTGATGGGTCGCCTGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCG‑ATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGATACCTACAAAGGCAAAATGAGCAAA  >  NC_002947/2272935‑2273228

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑