Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,774,626	0	A	.	21.5%	187.2 / 47.0	65	coding (1309/1704 nt)	yfjW	CP4‑57 prophage; putative inner membrane protein
Reads supporting (aligned to +/- strand):  ref base A (28/23);  new base . (9/5);  total (37/28)
Fisher's exact test for biased strand distribution p-value = 7.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

TACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAA  >  NC_000913/2774530‑2774723                                                                                                 |                                                                                                  tACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATaaaa                                                                                                >  1:714318/1‑100 (MQ=255) tACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATaaaa                                                                                                <  2:1042696/100‑1 (MQ=255)     tAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATaaaaaaa                                                                                             <  1:87743/99‑1 (MQ=255)     tAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAc                                                                                            <  1:888922/100‑1 (MQ=255)     tAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAAc                                                                                            <  1:476470/100‑1 (MQ=255)      aaCGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACa                                                                                           >  1:1065613/1‑100 (MQ=255)       aCGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTTCGTTCTATaaaaaacata                                                                                          >  2:566545/1‑96 (MQ=255)       aCGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATaaaaaacata                                                                                          >  2:1063470/1‑96 (MQ=255)         gggTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATAc                                                                                        >  1:917562/1‑100 (MQ=255)             tttttACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGa                                                                                    <  2:765718/100‑1 (MQ=255)                ttACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGc                                                                                 <  1:632525/100‑1 (MQ=255)                  aCTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCtt                                                                               >  1:1084586/1‑100 (MQ=255)                   cTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACACACCAGAAGCTTg                                                                              <  2:692569/100‑1 (MQ=255)                    ttGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGCCTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGa                                                                             >  2:610794/1‑100 (MQ=255)                    ttGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGa                                                                             <  1:1048269/100‑1 (MQ=255)                    ttGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑AAAAAACATACCAGAAGCTTGAt                                                                            >  2:767423/1‑100 (MQ=255)                     tGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGAt                                                                            >  2:651974/1‑100 (MQ=255)                     tGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGAt                                                                            >  1:995734/1‑100 (MQ=255)                         cTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑AAAAAACATACCAGAAGCTTGATAAAat                                                                       >  2:1236753/1‑100 (MQ=255)                         cTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑AAAAAACATACCAGAAGCTTGATAAAat                                                                       >  2:1235026/1‑100 (MQ=255)                          tAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAat                                                                       <  2:1235763/100‑1 (MQ=255)                          tAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAat                                                                       >  1:549287/1‑100 (MQ=255)                          tAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAat                                                                       >  2:1235540/1‑100 (MQ=255)                          tAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑AAAAAACATACCAGAAGCTTGATAAAata                                                                      <  2:74290/100‑1 (MQ=255)                           aaaaCCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAata                                                                      >  2:282815/1‑100 (MQ=255)                             aaCCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAatata                                                                    <  1:1266181/100‑1 (MQ=255)                               ccAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATATAAAAACATACCAGAAGCTTGATAAAATATatg                                                                  <  1:1236285/100‑1 (MQ=255)                               ccAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑AAAAAACATACCAGAAGCTTGATAAAATATatga                                                                 >  2:951020/1‑100 (MQ=255)                               ccAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑AAAAAACATACCAGAAGCTTGATAAAATATatga                                                                 >  2:951253/1‑100 (MQ=255)                                 aGATGATATTATTAATTACAACAATATCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATatga                                                                 <  2:1238032/99‑1 (MQ=255)                                 aGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATatgat                                                                <  1:1251667/100‑1 (MQ=255)                                    tgatATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGAc                                                             <  1:139552/100‑1 (MQ=255)                                       tattatTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATa                                                          >  2:494320/1‑100 (MQ=255)                                       tattatTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATa                                                          <  1:556514/100‑1 (MQ=255)                                        attattAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATaa                                                         >  2:619588/1‑100 (MQ=255)                                        attattAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑AAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAg                                                        >  1:404203/1‑100 (MQ=255)                                          tattaATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGc                                                       >  1:372120/1‑100 (MQ=255)                                          tattaATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑AAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCa                                                      >  1:285411/1‑100 (MQ=255)                                              aattaCAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATg                                                   >  2:657685/1‑100 (MQ=255)                                               attaCAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATgg                                                  >  2:704997/1‑100 (MQ=255)                                                ttaCAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGa                                                 >  1:554629/1‑100 (MQ=255)                                                   caacaaTAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGaaaa                                              >  1:1121254/1‑100 (MQ=255)                                                   caacaaTAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGaaaa                                              >  2:1231178/1‑100 (MQ=255)                                                      caaTAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTa                                           <  1:610798/100‑1 (MQ=255)                                                       aaTAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑AAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATc                                         <  1:951261/100‑1 (MQ=255)                                                       aaTAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTAT‑AAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATc                                         <  1:951028/100‑1 (MQ=255)                                                        aTAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATc                                         <  1:789260/100‑1 (MQ=255)                                                        aTAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATc                                         >  1:415730/1‑100 (MQ=255)                                                         tAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCt                                        <  1:651978/100‑1 (MQ=255)                                                          aGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCtt                                       <  2:246114/100‑1 (MQ=255)                                                          aGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCtt                                       <  2:683483/100‑1 (MQ=255)                                                           gCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTc                                      <  1:370543/100‑1 (MQ=255)                                                            cccTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCa                                     >  2:1280743/1‑100 (MQ=255)                                                                  cGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTgag                                <  2:1084576/99‑1 (MQ=255)                                                                  cGTACTACTCAAGACTGATTTTGCGTTCTAT‑AAAAAACATACCAGAAGCCTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGagag                              >  1:216415/1‑100 (MQ=255)                                                                      ctactCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCaa                           >  1:807770/1‑100 (MQ=255)                                                                         ctCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAg                        >  2:779564/1‑100 (MQ=255)                                                                         ctCAAGACTGATTTTGCGTTCTAT‑AAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAgg                       <  2:336680/100‑1 (MQ=255)                                                                           cAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGt                      >  1:519941/1‑100 (MQ=255)                                                                           cAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGt                      <  1:705001/100‑1 (MQ=255)                                                                           cAAGACTGATTTTGCGTTCTAT‑AAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCGCTGAGAGCAACAGGTa                     >  2:760566/1‑100 (MQ=255)                                                                                cTGATTTTGCGTTCTATAAAAAAACATACCATAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTAtct                  >  1:496943/1‑99 (MQ=255)                                                                                cTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTAtctc                 <  1:17261/100‑1 (MQ=255)                                                                                    ttttGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAg             <  1:7344/100‑1 (MQ=255)                                                                                      ttGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAAGTATCTTCACTGAGAGCAACAGGTATCTCCCAGtt           >  2:688596/1‑100 (MQ=255)                                                                                      ttGCGTTCTAT‑AAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGttt          <  2:404199/100‑1 (MQ=255)                                                                                         cGTTCTATAAAAAAACATACGAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAg        >  2:796847/1‑100 (MQ=255)                                                                                          gTTCTATAAAAAAACATACCCGAAGCCTTATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTAATAACAACAGGTATCTCACAGTTTaat       >  1:220000/1‑98 (MQ=255)                                                                                            tCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTAt     >  1:1222653/1‑100 (MQ=255)                                                                                             cTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATc    >  1:626229/1‑100 (MQ=255)                                                                                              tataAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGGAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCa   <  2:724099/100‑1 (MQ=255)                                                                                              tataAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCa   >  2:1258530/1‑100 (MQ=255)                                                                                               ataAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCaa  <  1:520739/100‑1 (MQ=255)                                                                                                 |                                                                                                  TACTTAACGGGTTTTTTACTTGTCCTAAAACCAGATGATATTATTAATTACAACAATAGCCCTTCCGTACTACTCAAGACTGATTTTGCGTTCTATAAAAAAACATACCAGAAGCTTGATAAAATATATGATGACATAAGCAATGGAAAATTATCTTCACTGAGAGCAACAGGTATCTCCCAGTTTAGTATCAA  >  NC_000913/2774530‑2774723

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑