Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,378,802	0	A	C	49.0%	73.9 / 12.4	51	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
Reads supporting (aligned to +/- strand):  ref base A (24/2);  new base C (0/25);  total (24/27)
Fisher's exact test for biased strand distribution p-value = 1.52e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAA  >  NC_000913/4378656‑4378941                                                                                                                                                        |                                                                                                                                            cTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑accgc                                                                                                                                         >  1:982611/1‑151 (MQ=255) cTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑accgc                                                                                                                                         >  2:315862/1‑151 (MQ=255)        aaTAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑accgccaccgcc                                                                                                                                  >  2:88353/1‑151 (MQ=255)                   caccaAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCggg                                                                                                                         >  1:777022/1‑149 (MQ=255)                           aCGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTttgtt                                                                                                               >  1:52415/1‑151 (MQ=255)                           aCGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTttgt                                                                                                                >  1:668931/1‑150 (MQ=255)                              caaGTAATTTTTTTGCGACCCGACCTTAACTAAAACACCTTTTGCTGGGTGGGGGGTTGTTTTTTGGGGATGTCCGCATA‑CCCCAGGTAAAATTAATAGGTTTTCCCC‑TA‑AT‑AAATT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGct                                                                                                            <  2:551839/149‑1 (MQ=255)                                   aatttttttGCTGCCCAACCCAACCTAAAAAATCGTTTGCTGTGTGACGGGCTGTTTTTTGGCGTTGCCCGCAGAGCCCGAGGA‑AAAGAAATAGGTTTTCCCT‑TA‑AT‑AATTT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCtata                                                                                                       <  2:574359/146‑1 (MQ=255)                                     aTGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCtata                                                                                                       >  2:500365/1‑149 (MQ=255)                                           tGCTGACCAACCCTAACTAAAACAACGTTTGTTGGGGGACGGGCTGTTTTGTGGGGATGCCCGTATACCCCCAGAA‑AAAGTAAAAGGGTTTCCCC‑GG‑AT‑AATTT‑CCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCgggg                                                                                                <  2:78595/150‑1 (MQ=255)                                             cTGCCCGACCCTAACCCAACCAACTTTTGCGGTGTGAGGGGCTGTTTTTTGGCGATGTCCCCATCGCCCCAGGA‑AAAGAAATAAGTTTTCCCT‑TA‑AA‑AATTT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCg                                                                                                   <  1:128807/145‑1 (MQ=255)                                                   gAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATtgtg                                                                                        >  1:554508/1‑150 (MQ=255)                                                     aCCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCg                                                                                      >  2:216081/1‑150 (MQ=255)                                                        tAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGc                                                                                  >  1:612898/1‑151 (MQ=255)                                                          aCTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGcac                                                                                >  2:43485/1‑151 (MQ=255)                                                              aaaccgggttggttgtgtgGGGGGCTGTTTTGTGGGGTTGCCCAAACAGCCCCAGAA‑AAATAAATAGTGTTTCCCG‑AA‑AA‑AAGTC‑ACCGCAACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGca                                                                                 <  1:224350/133‑1 (MQ=255)                                                              aaaCAGCGTTTGTTGTGGGACGGGTTTTTTTTTGGCGATGCCCGCATAGCCCCAGGA‑AAAGTAATAAGTTTTACCT‑TA‑AA‑AATTT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATg                                                                                   <  2:53276/144‑1 (MQ=255)                                                              aaaCAACTTTTGCTGTGTGACGGGCTGTTTTTTGGCGATGCCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTCCCC‑TG‑AT‑AAATT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCg                                                                                      <  2:100268/141‑1 (MQ=255)                                                               aacactttttGCTGTGTGAGGGGTTTTTTTTGGGCGATGCCCGAAAAGCCCAGGGA‑AAAGAAATAGGTTTTCCCC‑TA‑AA‑AAATT‑CCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAatat                                                                           <  2:946612/144‑1 (MQ=255)                                                               aacaccTTTTGCTGTGTGACGGGTTGTTTTTTGGCGATGCCCGCTTACCCCCAGGT‑AAAATAATAAGTTTTCCCT‑TA‑AA‑AAATT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAatat                                                                           <  2:10439/151‑1 (MQ=255)                                                               aaaatcttttGCTGTGTGGCGGGTTTTTTTTTGGGTATCCCCCAAGACCCCAAGGA‑AAAGAAAAAAGTTTTCCCC‑TA‑AT‑AATTC‑CCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACaa                                                                              <  1:293970/141‑1 (MQ=255)                                                                  agcttttGTTGGGTGGGGGGCTGTTTTTGGGCGATCCCCCAATCGCCCAGGGT‑AAAGTAATAGGGTTT‑CCC‑TGAAA‑AAATC‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCg                                                                         <  1:20287/146‑1 (MQ=255)                                                                  accGTTTGTTGTGTGAGGGCCTTTTTTTTGGCGTTGCCCCAAACCCCCCAGTA‑AAAGTAATAGGTTTTCCCT‑TA‑AA‑AAATC‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATc                                                                          <  1:1000641/147‑1 (MQ=255)                                                                      tttCCTTTGTGAGGGCCTGTTTTTTGGCGATGCCCGCATCGCCCAAGAA‑AAAGTAATAGGTTTTCCCC‑TA‑AT‑AAATT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTg                                                                      <  2:268713/149‑1 (MQ=255)                                                                         gCTGTGTGAGGGGCTGTTTTTGGGCGATGCCCGCATACCCCAAGGA‑AAAGTAAAAAGTTTTCCCT‑TG‑AA‑AATTT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGAttt                                                                  <  2:18085/150‑1 (MQ=255)                                                                           tgtgtgACGGGCTGTTTTTTGGCAATGCCCGCATACCCCCAGG‑‑AAAATAAAAAGGTTTTCCCTTA‑AA‑AAATT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGAt                                                                    <  2:709917/146‑1 (MQ=255)                                                                                gACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAggg                                                          >  1:474070/1‑151 (MQ=255)                                                                                          tttttGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAAtg                                                >  1:92891/1‑151 (MQ=255)                                                                                           ttttGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAAtgt                                               >  1:853141/1‑151 (MQ=255)                                                                                            ttgggggATTTCCGCATGGCCCAAGG‑‑AAAATAAAAAAGTTTTCCC‑TT‑ATAAAATT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAAtgt                                               <  2:370729/144‑1 (MQ=255)                                                                                               ggCGATTCCCGCATACCCCCAGAA‑AAAGAAATAAGTTTTCCCT‑TA‑AT‑AATTT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGa                                            <  1:110982/150‑1 (MQ=255)                                                                                                   aTGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCa                                         >  1:939545/1‑149 (MQ=255)                                                                                                    tGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCa                                         >  2:174065/1‑148 (MQ=255)                                                                                                       ccGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGc                                   >  2:392617/1‑151 (MQ=255)                                                                                                          cATAGCCCCAGAA‑AAAGAAATAGGTTTTCCCC‑TG‑AT‑AATTC‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCg                                  <  1:271328/149‑1 (MQ=255)                                                                                                           aTAGCCCCAGGA‑AAAAAAAAAAGTTTTCCCT‑TG‑AT‑AAATC‑CCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCg                                  <  2:394916/148‑1 (MQ=255)                                                                                                            tAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGta                               >  2:64854/1‑150 (MQ=255)                                                                                                             aGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGtaat                             >  2:535768/1‑151 (MQ=255)                                                                                                                 ccAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGtaattaa                          >  2:603860/1‑150 (MQ=255)                                                                                                                  cAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGtaattaat                         >  1:306377/1‑150 (MQ=255)                                                                                                                      gaaaaaaaaaaaGGTTTTCCC‑CG‑AA‑AAATTCACCCCCGCCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGtaattaat                         <  1:1019786/138‑1 (MQ=255)                                                                                                                        aaaGTAATAAGTTTTCCCC‑TA‑AT‑AATTT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATtaataa                       <  2:734505/147‑1 (MQ=255)                                                                                                                         aaGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGgcgc                  >  1:609830/1‑151 (MQ=255)                                                                                                                             aataaGTTTTCCCT‑AA‑AT‑AAATT‑CCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCaga               <  1:682735/150‑1 (MQ=255)                                                                                                                             aataaGTTTTCCCA‑TA‑AT‑AATTC‑CCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCag                <  1:500271/149‑1 (MQ=255)                                                                                                                             aataaGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCag                >  2:132611/1‑149 (MQ=255)                                                                                                                                 aGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGcg            >  2:822419/1‑149 (MQ=255)                                                                                                                                   gTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGcgtcg         >  1:234139/1‑150 (MQ=255)                                                                                                                                    gttttcccataaT‑AAATC‑CCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGcgtcg         <  1:945539/140‑1 (MQ=255)                                                                                                                                     ttttcccataaT‑AAATC‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGcgtc          <  1:774281/139‑1 (MQ=255)                                                                                                                                       aCCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGtttt     >  1:90933/1‑150 (MQ=255)                                                                                                                                        ccc‑TA‑AA‑AAATT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGa   <  2:52422/151‑1 (MQ=255)                                                                                                                                         cc‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGtttt     >  2:1016438/1‑148 (MQ=255)                                                                                                                                                  aaaTT‑CCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGaa  <  2:138668/145‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                            CTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTCAAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGT‑AAAGTAATAAGGTTTACCC‑TG‑AT‑AAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTTGAA  >  NC_000913/4378656‑4378941

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: ‑