Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,337,723	0	A	C	46.0%	78.2 / 19.6	51	G566G (GGT→GGG)	gyrA	DNA gyrase (type II topoisomerase), subunit A
Reads supporting (aligned to +/- strand):  ref base A (25/2);  new base C (0/23);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 5.55e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGCGCGCCACGAGTGGCTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTC  >  NC_000913/2337576‑2337863                                                                                                                                                     |                                                                                                                                             gcgcgcgcCACGAGTGGCTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCt                                                                                                                                           >  2:965070/1‑151 (MQ=255)  cgcgcgcCACGAGTGGCTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCtt                                                                                                                                          <  2:721993/151‑1 (MQ=255)      cgcCACGAGTGGCTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTccc                                                                                                                                      <  2:889394/151‑1 (MQ=255)            gAGTGGCTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCacg                                                                                                                                >  1:349499/1‑151 (MQ=255)            gAGTGGCTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCacg                                                                                                                                >  1:733895/1‑151 (MQ=255)              gTGGCTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCacgac                                                                                                                              >  2:804580/1‑151 (MQ=255)                  cTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTg                                                                                                                          >  2:1021316/1‑151 (MQ=255)                       gccAACTGAAAACCTTTCATCGAATAGACGCGACCACGGCTGGAAAAGCAAAGAATATGGTCGTGAGTGTC‑CCCCCCCAGCAGTCGGTCGATAAAGTTTTCTTCTTTAATACGTGCGGCAGTTTTCCCTTTCCCGCCACGACGCTGCGCt                                                                                                                      <  1:748676/148‑1 (MQ=255)                          aaCTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGt                                                                                                                  >  2:643023/1‑151 (MQ=255)                           aCTGATAAACTTTCATCAAATAGACGCGCCCCCGGCTGGAGAAGCAAAGAATATGGTCGTGAGTGTT‑CGCCACCAGCGGTCGGTCGATAAAGTCTTCTTCTTTAATCCGTGCGGAAGATTTCCCTTTCCCGCCACGACGCTGCGCTTc                                                                                                                    <  1:410673/148‑1 (MQ=255)                             tGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTAtt                                                                                                               >  2:72270/1‑151 (MQ=255)                                  aaCTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGa                                                                                                           >  2:289730/1‑150 (MQ=255)                                        cATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCgg                                                                                                     >  2:378514/1‑150 (MQ=255)                                        cATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGc                                                                                                    >  2:632230/1‑151 (MQ=255)                                        cATCAAAAAGACGCGCCCGCGGCAGGAGAAGCAAAGAATATGGTGGTGAGTTTT‑CGCCACCAGCAGGCGGTCAAAAAATTTTTCTTTTTTAATACGTGCGGCAGATTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCg                                                                                                      <  2:237559/149‑1 (MQ=255)                                         aTCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCt                                                                                                   >  2:68399/1‑151 (MQ=255)                                         aTCGAAAGGCCGCGACCCGGGCGGGAGAAGCACAAAATAGGGCCG‑GTGTGTTCCGCCACCAGCGGTCGGTCGAAAAATTCTTTTTCTTAAATACGTGGGGCAGATTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGc                                                                                                    <  1:844572/150‑1 (MQ=255)                                         aTCAAATAGACGCGCCCCCGGCGGGAAAAGCAAAAAATTGGGTGGTGAGTTTT‑CCCCACCAGCAGTCGGTCGATAAATTTTTCTTCTTTAATACGTGGGGAAGATTTCCTTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCt                                                                                                   <  1:895570/151‑1 (MQ=255)                                          tCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTg                                                                                                  >  2:878135/1‑151 (MQ=255)                                             aaTAGCCGCGCCCACGGCGGGAGAAGCACAAAATATGGTCGTGAGTGTC‑CGCCCCCAGCAGTCGGTCGAAAAAGTCTTCTTCTTTAATACGTGCGGAAAATTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATa                                                                                               <  1:754192/151‑1 (MQ=255)                                                aGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACtt                                                                                            >  1:599490/1‑151 (MQ=255)                                                     cgACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGt                                                                                       >  1:818990/1‑151 (MQ=255)                                                      gACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGt                                                                                       >  1:776478/1‑150 (MQ=255)                                                         cagggCTGGAGAAGCACAGAATATGTTCGTGGGTGTC‑CGCCCCCAGCAGTCGTTCGATAAGGTCTTCTTTTTTAATCCGTGCGGCAGATTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTa                                                                                      <  1:76921/145‑1 (MQ=255)                                                            ggCTGGAGAAGCACAGAATATGGTCGTGAGTTTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATCCGTGCGGAAGATTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGccc                                                                                  <  2:44176/149‑1 (MQ=255)                                                            ggCTGGAGAAGCACAAAATTTGGTCGTGGGTTTT‑CGCCACCAGCAGCCGGTCGATAAATTCTTCTTCTTTAATACGTGCGGCAAATTTCCTTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCt                                                                                 <  2:194582/150‑1 (MQ=255)                                                                    aatcacaGAATTTGTTGGGGAGTGTT‑CGCCCCCACAAGTGGTTCGAAAAGGTCTTCTTTTTTAATTCGGGCGAAAGATTTCCTTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTgaga                                                                          <  1:1003462/146‑1 (MQ=255)                                                                    aaccacaAAATTTGGTCGTGATTGTT‑CGCCCCCAGGAGTCGGTCGATAAAGTTTTCTTCTTTAATACGTGCGGAAGATTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTgagaga                                                                        <  1:492818/148‑1 (MQ=255)                                                                    aaGCACAGAATATGGTCGGGAGTGTT‑CCCCCCCAGCAGTCGGTCGATAAAGTCTTTTTCTTTAATACGTGCGGAAGATTCCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGt                                                                              <  2:423250/145‑1 (MQ=255)                                                                     aGCACAGAATATGGTTGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTgagag                                                                         >  1:282050/1‑149 (MQ=255)                                                                       cacaGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCg                                                                     >  1:182124/1‑151 (MQ=255)                                                                         caGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTc                                                                   >  2:1044089/1‑151 (MQ=255)                                                                          aGAATATGGTCGTGAGTGTC‑CCCCCCCAGCGGTCGGTCAAAAAATTCTTCTTCTTTATTACGGGCGGAAGTTTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGt                                                                    <  1:959765/149‑1 (MQ=255)                                                                                        aGTGTT‑CCCCCCCAGCAGTCGGTCGAAAAAGTCTTCTTTTTTAATACGTGCGGCAGATTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCtt                                                      <  2:489621/149‑1 (MQ=255)                                                                                           tgtccccccccaGCAGTGGGTAAAAAAATTCTTTTTTTTAAATCCGTGCGGCAGTTTTCCTTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCtt                                                      <  1:609104/138‑1 (MQ=255)                                                                                           gtT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTgg                                                 >  1:967819/1‑151 (MQ=255)                                                                                               ccccaccaGCAGTCGGTCAATAAACTTTTTTTTTTTAATACGTGCGGCAGTTTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTcc                                                    <  1:499736/143‑1 (MQ=255)                                                                                                 ccaccaGCAGTCGTTCGAAAAAGTCTTCTTTTTTAATTCGTGCGGAAGATTTCCTTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGa                                             <  2:6032/150‑1 (MQ=255)                                                                                                 ccaccaGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGAt                                            >  1:138433/1‑151 (MQ=255)                                                                                                             ggtggATAAAGTTTTCTTTTTAAATACGTGCGGAAGTTTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCt                                     <  2:558791/146‑1 (MQ=255)                                                                                                             ggtcgATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTcc                                  >  2:627375/1‑149 (MQ=255)                                                                                                                    aatttcttcttctTTATTTGGTGCGGCACTTTCGCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTc                                   <  2:674362/137‑1 (MQ=255)                                                                                                                     aaGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGt                        >  2:274608/1‑151 (MQ=255)                                                                                                                         cttcttcttTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTgc                    >  1:851536/1‑151 (MQ=255)                                                                                                                          tttttcttTAAACCGGGCGGAAAATTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTgc                    <  2:581842/147‑1 (MQ=255)                                                                                                                                  tAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGc           >  2:924324/1‑151 (MQ=255)                                                                                                                                  tAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGc           >  1:453588/1‑151 (MQ=255)                                                                                                                                   aaTCCGTGCGGCAGATTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGc           <  2:999415/150‑1 (MQ=255)                                                                                                                                      aCGTGCGGAAGATTTCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGc           <  1:676091/147‑1 (MQ=255)                                                                                                                                        gTGCGGCAGATTTCCCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGa      <  2:322555/150‑1 (MQ=255)                                                                                                                                                 ttttCCCTTCCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTc  <  2:447575/144‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                             GCGCGCGCCACGAGTGGCTTCCGGCAACTGATAAACTTTCATCGAATAGACGCGACCACGGCTGGAGAAGCACAGAATATGGTCGTGAGTGTT‑CGCCACCAGCAGTCGGTCGATAAAGTCTTCTTCTTTAATACGTGCGGCAGATTTACCTTTCCCGCCACGACGCTGCGCTTCGTATTCAGAAAGCGGCTGATACTTAACGTAGCCCTGGTGAGAGAGCGTCACGACCACATCTTCCTGGGTGATCAGATCTTCCAGGTTGATGTCTGCGCTGTTGGCGGTGATTTC  >  NC_000913/2337576‑2337863

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑