Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,254	0	A	T	20.7%	104.3 / 25.1	58	intergenic (+258/‑325)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base A (29/17);  new base T (6/6);  total (35/23)
Fisher's exact test for biased strand distribution p-value = 5.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.23e-01

TAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGC  >  NC_007790/1156‑1353                                                                                                   |                                                                                                    tAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaat                                                                                                    >  1:822801/1‑100 (MQ=255) tAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaat                                                                                                    >  1:3139948/1‑100 (MQ=255) tAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaat                                                                                                    >  1:5526149/1‑100 (MQ=255) tAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaat                                                                                                    >  1:25509/1‑100 (MQ=255) tAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaat                                                                                                    >  1:2183639/1‑100 (MQ=255) tAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGaaaaattaaaaat                                                                                                    >  1:567483/1‑100 (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                                                                                                  >  1:4246202/1‑100 (MQ=255)   aaaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtc                                                                                                  >  1:6063694/1‑100 (MQ=255)   aaaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtc                                                                                                  >  1:3009851/1‑100 (MQ=255)    taCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtct                                                                                                 >  1:3969092/2‑100 (MQ=255)    aaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAGAATTAAAAATtct                                                                                                 >  1:4112816/1‑100 (MQ=255)    aaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtct                                                                                                 >  1:5841179/1‑100 (MQ=255)    aaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtct                                                                                                 >  1:4380276/1‑100 (MQ=255)    aaCCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATtct                                                                                                 >  1:5563216/1‑100 (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                                                                            >  1:2413220/1‑100 (MQ=255)                         tGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGcc                                                                            >  1:3789201/1‑100 (MQ=255)                          gCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGccc                                                                           >  1:4601414/1‑100 (MQ=255)                             aGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGTTAAAAAACGCCCTGc                                                                        <  1:4875324/100‑1 (MQ=255)                             aGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGc                                                                        <  1:5705968/100‑1 (MQ=255)                             aGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGc                                                                        <  1:881905/100‑1 (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                                                  >  1:2604232/1‑100 (MQ=255)                                                   aGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTgg                                                  <  1:5846947/100‑1 (MQ=255)                                                   aGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTgg                                                  <  1:4501576/100‑1 (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)                                                                                                   attCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGc  <  1:2041515/100‑1 (MQ=255)                                                                                                   attCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGc  <  1:5554530/100‑1 (MQ=255)                                                                                                   attCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGc  <  1:2553698/100‑1 (MQ=255)                                                                                                   attCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGc  <  1:1751886/100‑1 (MQ=255)                                                                                                   attCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGc  <  1:318087/100‑1 (MQ=255)                                                                                                   attCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGc  <  1:4229313/100‑1 (MQ=255)                                                                                                   attCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGc  <  1:483517/100‑1 (MQ=255)                                                                                                   |                                                                                                    TAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCAAATTCTCCTTATGCTCTTACGGAGTTTTTAGAGAAAAATTAAAAATTCTCGATTTTTGATAAAAAACGCCCTGCAGGAATTTAGAAAAACATGTGGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCATGTAAATGGGC  >  NC_007790/1156‑1353

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑