Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,244	0	A	T	21.1%	107.2 / 24.9	58	intergenic (+248/‑335)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base A (29/16);  new base T (6/6);  total (35/23)
Fisher's exact test for biased strand distribution p-value = 5.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.19e-01

AAATACCTTAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTA  >  NC_007790/1148‑1328                                                                                                 |                                                                                     cagtACCTTAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaa                                                                                   >  1:3235218/4‑100 (MQ=255)  cctACCTTAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaat                                                                                  >  1:1174902/3‑100 (MQ=255)   gtACCTTAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaatt                                                                                 >  1:1073812/2‑100 (MQ=255)    tACCTTAAAACCCCTGGAATTTCTGGTTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaatta                                                                                >  1:2151523/1‑100 (MQ=255)     aCCTTAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaa                                                                               >  1:1619938/1‑100 (MQ=255)     aCCTTAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaa                                                                               >  1:2695455/1‑100 (MQ=255)     aCCTTAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaa                                                                               >  1:4170948/1‑100 (MQ=255)         tAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaat                                                                           >  1:3139948/1‑100 (MQ=255)         tAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaat                                                                           >  1:567483/1‑100 (MQ=255)         tAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaat                                                                           >  1:5526149/1‑100 (MQ=255)         tAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaat                                                                           >  1:25509/1‑100 (MQ=255)         tAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaat                                                                           >  1:2183639/1‑100 (MQ=255)         tAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaat                                                                           >  1:822801/1‑100 (MQ=255)          aaaaCTCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaatt                                                                          >  1:3919708/1‑100 (MQ=255)          aaaaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaatt                                                                          >  1:4243245/1‑100 (MQ=255)          aaaaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaatt                                                                          >  1:4355439/1‑100 (MQ=255)           taaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtc                                                                         >  1:4719556/2‑100 (MQ=255)           caaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtc                                                                         >  1:6037893/2‑100 (MQ=255)           aaaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCACATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtc                                                                         >  1:5638526/1‑100 (MQ=255)           aaaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtc                                                                         >  1:3009851/1‑100 (MQ=255)           aaaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtc                                                                         >  1:4246202/1‑100 (MQ=255)           aaaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtc                                                                         >  1:6063694/1‑100 (MQ=255)            taCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtct                                                                        >  1:3969092/2‑100 (MQ=255)            aaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAGAATTAAAAATtct                                                                        >  1:4112816/1‑100 (MQ=255)            aaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtct                                                                        >  1:5841179/1‑100 (MQ=255)            aaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtct                                                                        >  1:5563216/1‑100 (MQ=255)            aaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtct                                                                        >  1:4380276/1‑100 (MQ=255)               cccTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGa                                                                     >  1:4824290/1‑100 (MQ=255)                           tGGCCTTGCCAGATCTATCATTTTTGAATGATAGCAAATTTCCCTTATGCTCTTACGGAGATTTTAGAGTTAAATTAAAATTTCTAAGTTTTTGATaaga                                                         >  1:1896749/1‑98 (MQ=255)                                ttGCCTGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGc                                                    >  1:3377329/1‑100 (MQ=255)                                ttGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGc                                                    >  1:4571345/1‑100 (MQ=255)                                ctGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGc                                                    >  1:3893652/2‑100 (MQ=255)                                 tGCCAGATCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGcc                                                   >  1:4698578/1‑100 (MQ=255)                                 tGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGcc                                                   >  1:1838983/1‑100 (MQ=255)                                 tGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGcc                                                   >  1:3789201/1‑100 (MQ=255)                                 tGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGcc                                                   >  1:2413220/1‑100 (MQ=255)                                  gCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGccc                                                  >  1:4601414/1‑100 (MQ=255)                                     aGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGTTAAAAAACGCCCTGc                                               <  1:4875324/100‑1 (MQ=255)                                     aGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGc                                               <  1:881905/100‑1 (MQ=255)                                     aGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGc                                               <  1:5705968/100‑1 (MQ=255)                                      gatcTATCATTTTTGAATGATAGCAAATTTCCCTTATGCTCTTACGGAGATTTTAGAGTTAAATTAAAATTTCTAAGTTTTTGATAAGAAAAGCCCTGcc                                              <  1:3898845/97‑2 (MQ=255)                                      gatcTATCATTTTTGAATGATAGCAAATTTCCCTTATGCTCTTACGGAGATTTTAGAGTTAAATTAAAATTTCTAAGTTTTTGATAAGAAAAGCCCTGCa                                              <  1:4034201/97‑1 (MQ=255)                                      gACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCa                                              <  1:1360217/100‑1 (MQ=255)                                        ccTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAgg                                            <  1:5620708/100‑1 (MQ=255)                                        ccTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAgg                                            <  1:5327700/100‑1 (MQ=255)                                         cTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAggc                                           <  1:1827726/100‑2 (MQ=255)                                          tATCATTTTTGAATGATAGCAAATTTCCCTTATGCTCTTACGGAGATTTTAGAGTTAAATTAAAATTTCTAAGTTTTTGATAAGAAAAGCCCTGCAGGag                                          <  1:3582634/100‑2 (MQ=255)                                          tATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAggca                                          <  1:3294638/100‑3 (MQ=255)                                             cATTTTTGAATGATAGCAAATTTCCCTTATACTCTTACGGAGATTTTAGAGTTAAATTAAAATTTCTAAGTTTTTGATAAGAAAAGCCCTGCAGGAAttt                                       <  1:3833815/100‑1 (MQ=255)                                             cATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAAttt                                       <  1:2606118/100‑1 (MQ=255)                                                ctttGAATGATAGCAAATTTCCCTTATGCTCTTACGGAGATTTTAGAGTTAAATTAAAATTTCTAAGTTTTTGATAAGAGAAGCCCTGCAGGAATTTCGa                                    >  1:3351697/2‑100 (MQ=255)                                                   tGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGaaaa                                 >  1:5032513/1‑100 (MQ=255)                                                       acaTAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACAt                             >  1:2972342/3‑100 (MQ=255)                                                        gctcttccgatctcCTTA‑GCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACAtgt                           <  1:4598546/90‑1 (MQ=255)                                                         aTAGCAAATTCTCCTTATTCTCTTTCCTCTTTTTTTCATCGGAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACAtgt                           <  1:191030/100‑1 (MQ=255)                                                         aTAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACAtgt                           <  1:5435128/100‑1 (MQ=255)                                                           aGCAAATTCTCCTTATGCTCTTACGGAGTTTTTATAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGCgg                         >  1:4628032/1‑100 (MQ=255)                                                           aGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTgg                         >  1:206121/1‑100 (MQ=255)                                                           aGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTgg                         <  1:5846947/100‑1 (MQ=255)                                                           aGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTgg                         <  1:4501576/100‑1 (MQ=255)                                                           aGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTgg                         >  1:2604232/1‑100 (MQ=255)                                                            gCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGa                        <  1:2166846/100‑1 (MQ=255)                                                                cttCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCATGCAGGAATTTAGAAAAACAtgaagatcgg                    >  1:3146462/2‑92 (MQ=255)                                                                atctcccTTATGCTCTTACGGAGATTTTAGAGTTAAATTAAAATTTCTAAGTTTTTGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACACGGGGAAgat                    >  1:454737/6‑98 (MQ=255)                                                                    cccTTATGCTCTTACGGAGATTTTAGAGTTAAATTAAAATTTCTAAGTTTTTGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTaa                >  1:529199/2‑100 (MQ=255)                                                                     ccTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTaaa               >  1:4999/1‑100 (MQ=255)                                                                     ccTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTaaa               >  1:2234740/1‑100 (MQ=255)                                                                        tATGCTCTTACGGAGATTTTAGAGTTAAATTAAAATTTCTAAGTTTTTGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAgta            >  1:613103/1‑98 (MQ=255)                                                                          tGCTCTTACGGAGATTTTAGAGTTAAATTAAAATTTCTAAGTTTTTGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTAtt          <  1:443702/100‑1 (MQ=255)                                                                              ctTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCGTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTAt      >  1:1673216/1‑100 (MQ=255)                                                                                tACGGAGATTTTAGAGTTAAATTAAAATTTCTAAGTTTTTGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGc    >  1:5181457/1‑100 (MQ=255)                                                                                 aCGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCt   <  1:2884971/100‑1 (MQ=255)                                                                                  gatctattttAGAGTTAAATTAAAATTTCTAAGTTTTTGATAAGAAAAGCCCTGCAGGAATTTAGAAAAACATGGGGAAGTTTTAAAGTATTTTATGCTa  <  1:4265745/94‑1 (MQ=255)                                                                                  atctgTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTa  <  1:3848789/96‑1 (MQ=255)                                                                                                 |                                                                                     AAATACCTTAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTA  >  NC_007790/1148‑1328

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑