Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	17,041	0	G	C	43.1%	69.9 / 18.6	51	intergenic (‑81/‑448)	mokC/nhaA	regulatory protein for HokC, overlaps CDS of hokC/sodium‑proton antiporter
Reads supporting (aligned to +/- strand):  ref base G (17/12);  new base C (0/22);  total (17/34)
Fisher's exact test for biased strand distribution p-value = 3.66e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATT  >  NC_000913/16895‑17184                                                                                                                                                   |                                                                                                                                                ctgctTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTc                                                                                                                                             >  1:663802/1‑151 (MQ=255)      tCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGc                                                                                                                                         <  1:366296/150‑1 (MQ=255)       cATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCAc                                                                                                                                       >  2:506095/1‑151 (MQ=255)          tGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCAccc                                                                                                                                     <  1:1099343/150‑1 (MQ=255)               tcttctCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCt                                                                                                                               >  2:151108/1‑151 (MQ=255)                cttctCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCt                                                                                                                               >  2:237451/1‑150 (MQ=255)                            cTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGctc                                                                                                                   >  1:843625/1‑150 (MQ=255)                                 ggTAAGTAAGAGCCCCTCTACTTGTGTTCAGCATATAGGAGGCCTCGGTTTGATGGAAAAATACCCCTCGGGGTTTTTCTTTATCTCCCGTTCAGCTAATGCCTGAGACAGCCAGCCCCAAGCACCCGCCGCTATTATATCGCTCTCTTTa                                                                                                             <  1:1071453/151‑1 (MQ=255)                                 ggTAAGAAAGAGGCCCTCTACATTTTTTAAGCATATGGGGGCCCTGGGGTTGTTGAAAAAATATCCCCCGGTTTTTTTCTCTCCCGCCCTTTCAGTTACTCCCTGAGACAAACACCCTAAACCCCCCGCCGCTATTATATCGctctct                                                                                                                <  2:203168/148‑1 (MQ=255)                                 ggTAAGAAAGAGGCACTCTACATGTGTTCAGAATATGGGAGGCCTGGGTTTGATGAAAAAATATCCCGCGGGTTTTTTCTCTTTCTGCCGTTCAGATAAGGCCTGAGACAGACACCCCCAAGCACCCGCCGCTATTATATCGCTCTCttt                                                                                                              <  1:238994/150‑1 (MQ=255)                                      gTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAAccc                                                                                                         >  2:261123/1‑150 (MQ=255)                                            ggCACTCTACATGTGTTCAGCATATAGGAGGCCTGGGGTTGATGGAAAAATATCCCTGGGGGTTTTTCTCTATCTGCCTTTCAGCTAATGCCGGAGACAGACACCCCCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGt                                                                                                  <  1:782176/151‑1 (MQ=255)                                             gCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGtt                                                                                                 >  2:996212/1‑151 (MQ=255)                                                ctctACATGTGTTCAGCATATAGGGGCCCGGGGTTTGAGGAAAAAATACCCCTGGGGTTTTTTCTCTATCCCCTGTTCAATTATCCCCTGAGACAGACAGCTTCACGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGtttt                                                                                               <  2:840131/150‑1 (MQ=255)                                                 tctACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTAt                                                                                             >  2:60899/1‑151 (MQ=255)                                                    actttttttaagaatatGGGGGCCCTGGGTTTGATGAAAAAATATCCCGGGGGTTTTTTCTCTATCTCCCGTTCATCTAAGGCCTGAGACACCCAGCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCAtttt                                                                                                    <  2:633396/128‑1 (MQ=255)                                                    aCATGTTTTCAGAATATAGGAGGCCTGGGTTTGATGAAAAAATATCACTCGGGGTTTTTCTCTTTCTGCCTTTCATCTAATGCCGGAGACAGACACCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCg                                                                                           <  1:921434/150‑1 (MQ=255)                                                      aTGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGAtt                                                                                        >  1:86084/1‑151 (MQ=255)                                                        gtgtTCAGCATATAGGGGGCCTGGGTTTGATGAAAAAATACCCCCCGGGGTTTTTCTCTATCGCCCGTTCAGCTAATGCCGGAGACAGACACCCTAAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGa                                                                                          <  1:127244/147‑1 (MQ=255)                                                         ttttCAGAATAGGGGGGCCCTGGGGTTGATGAAAAAATATCCCTCGGGGTTTTTCTCTATCTGCCTTTCAGCTAATCCCTGAGACAGACACCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCt                                                                                      <  1:957721/148‑1 (MQ=255)                                                           ttaaacATATGGGGGCCCGCGGGTTGATGAAAAAATCTCCCCCGGGGTTTTCCTCTTCCTGCCTTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGAtt                                                                                        <  2:663819/141‑1 (MQ=255)                                                           tgcagtataagggagcCCTGGGTTTAATAATAAAATATCCCTCGGGTTTTTTCTCTCCCTGCTTTTAAGCTAATCCCTGACACACACACCCACAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTa                                                                                     <  2:250863/138‑1 (MQ=255)                                                             cAGCATATGGGGGGCCGCGGTTTGATGGAAAAATACCACTGGGGGTTTTTCTCTATCTGCCTTTCATCTAATGCCTGAGAAAGCCAGCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCt                                                                                      <  2:381450/146‑1 (MQ=255)                                                                      gggggCCTGGGGTTGATGATAAAATATCCCTCGGGGTTTTTCTCTATCTGCCGTCCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAg                                                                            <  1:274261/144‑1 (MQ=255)                                                                      ggggcccTGGGTTTGATGAAAAAATACCCCGCGGGTTTTTTCTCTATCTCCCTTTCAGCTAATGCCTGAGACAGACACCCTCAACCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGc                                                                        <  2:676151/146‑1 (MQ=255)                                                                      ggaggCCTGGGGTTGATGGAAAAATACCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCAGAGACAGACGCCCTCAATCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGAc                                                                          <  1:749927/149‑1 (MQ=255)                                                                      ggaggCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGc                                                                        >  1:85048/1‑151 (MQ=255)                                                                      ggaggCCTCGGGTTGATGATAAAATACCCCTCGGGGTTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACACCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACg                                                                         <  1:151098/150‑1 (MQ=255)                                                                      ggagcCCTGGGTTTGAGGAAAAAATCCCCCTGGGGTTTTTTCTCTATCTGCCTTTCAGTTAAGCCCTGAAACACCCACCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGa                                                                           <  2:826221/148‑1 (MQ=255)                                                                      ggagcCCTGGGGTTAAGGAAAAAATATCACTGGGGCCTTTTCTCTTTCTGCCGTTCAGCTAAGGCCAGAACCAGCCAGCCCCACCCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGAc                                                                          <  1:108722/149‑1 (MQ=255)                                                                           ccTGGGGTTGATGGAAAAATATCACTCGGGGTTTTTCTCTTTCTGCCGTTCAGCTAATGCTTGAGACAGACAGCCCCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGc                                                                   <  1:354973/151‑1 (MQ=255)                                                                               gggTTGATGAAAAATTACCCCTGGGTTTTTTTCTCTTCCTCCCTTTAACCTAATGCCTGAGACAGCCACCCTCAACCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCAtt                                                                <  2:238182/150‑1 (MQ=255)                                                                                          aaaaTATCCCTGGGGGTTTTTCTCTTTCTGCCGTTAAGCTAATGCCTGAGACAGACACCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTtg                                                            <  1:506089/143‑1 (MQ=255)                                                                                          aaaaTATCCCTCGGGTTTTTTCTCTATCTCCCGTTCAGCTATGCCCTGAGACAGCCACCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGc                                                        <  1:764822/147‑1 (MQ=255)                                                                                          aaaaTACCCCTCGGGTTTTTTCCTTCTCTGCCTTCCAGCTAATCCCTAAGAAAGACACCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTgg                                                         <  2:91557/146‑1 (MQ=255)                                                                                          aaaaTACCACTCGGGTTTTTTCTCTATCTGCCTTTCAGTTAATGCCTGAAACAGACAGCCTAAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCAttttt                                                             <  2:577436/142‑1 (MQ=255)                                                                                            aaTATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAAtt                                                  >  1:496061/1‑151 (MQ=255)                                                                                              tatCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAAtttt                                                >  2:384301/1‑151 (MQ=255)                                                                                                     cGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATg                                          >  1:180998/1‑150 (MQ=255)                                                                                                      ggggTTTTTCTTTATCTCCCTTTCAGCTATTGCCTGAGACAGACAGCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAAt                                           <  1:543732/148‑1 (MQ=255)                                                                                                      ggggTTTTTCTCTATCTGCCTTTCAGCTAATGCCTGAGACAGACACCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAAt                                           <  1:167876/148‑1 (MQ=255)                                                                                                        ggCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGAttt                                      >  2:814544/1‑151 (MQ=255)                                                                                                           ttttCTCTATCTGCCTTCCAATAAATCCCTAAAAAAGACACCTTCAACCCACCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTAGCGTAATTTTTTAATGATTTaa                                    <  2:851583/150‑1 (MQ=255)                                                                                                                        ccGTTCAGTTAATGCCTGAGAAAGACACCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACttt                        <  1:544838/149‑1 (MQ=255)                                                                                                                          gTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAAtt                    >  2:642765/1‑151 (MQ=255)                                                                                                                           ttCAGCTAATCCCTGAGACAGCCACCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAAtt                    <  2:183083/150‑1 (MQ=255)                                                                                                                            tCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAAttt                   >  1:1003081/1‑150 (MQ=255)                                                                                                                            tCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAAttt                   >  2:771894/1‑150 (MQ=255)                                                                                                                              agcaattGCCTAAAAAAGACACCCTAAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTAtc                <  2:753610/145‑1 (MQ=255)                                                                                                                                  attcccTGAGACAGACACCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTAtc                <  1:826154/143‑1 (MQ=255)                                                                                                                                      ctctagccacacatCCCCAACCGCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTAAATTATTTAACTTTAATTTATCTCTTCAt         <  1:461141/140‑1 (MQ=255)                                                                                                                                      ccTGAGACAACCACCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTc           <  1:130401/148‑1 (MQ=255)                                                                                                                                          agaaacacacCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCAt         <  2:896037/140‑1 (MQ=255)                                                                                                                                            acagccacCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAatt  <  2:496064/151‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                CTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATT  >  NC_000913/16895‑17184

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑