Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	573,403	0	T	C	44.2%	52.2 / 14.9	43	P11P (CCT→CCC)	rusA	DLP12 prophage; endonuclease RUS
Reads supporting (aligned to +/- strand):  ref base T (20/4);  new base C (0/19);  total (20/23)
Fisher's exact test for biased strand distribution p-value = 1.65e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCATTG  >  NC_000913/573253‑573548                                                                                                                                                       |                                                                                                                                                  gccACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCt                                                                                                                                                   <  2:453743/151‑1 (MQ=255)   cACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTcc                                                                                                                                                 >  1:190211/1‑151 (MQ=255)      gacgaAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAg                                                                                                                                              <  2:146041/151‑1 (MQ=255)              cGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCaataat                                                                                                                                       <  2:48143/150‑1 (MQ=255)               gACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCg                                                                                                                                     >  2:557925/1‑151 (MQ=255)                               ttgttgACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATaa                                                                                                                      >  2:739740/1‑150 (MQ=255)                                                  aaaaaaagcggggggggAGGGTATGGGAAGAACAAAGGTTATTGGGCAAAAAGGGGGTGTTATTAGGGCGAGAATGCCTACAGCATACCATCCCCCTGCCCCCGAAGCAAAAAGCGCTTTTACCGCCATAATCGCGGGCGCACGCACGTCa                                                                                                  <  2:609587/136‑1 (MQ=255)                                                  aaaaaaATGCGGGCTGGAGGGTATGGGAAAAACACAGTTTATCTGGATAAAAGGGGGGTTTATAAAGGCGTGAATCCCAACAGCTCCACCTTCCCCGGCCCCCCGACCAATACCCGTTTTTACCGCCATAATCGCGGGCGCACGCACGTCa                                                                                                  <  2:840066/151‑1 (MQ=255)                                                          gcgggcggGAAGGTAGGGCGAAAACACAGTTTATCTGGCGGAAGGGGGGTTTTATAAGGGGGTAAATCCCAACACCATCACATTCCCCTGCCCCCCGAAAAAAAACCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCaga                                                                                           <  1:1005945/150‑1 (MQ=255)                                                          gcgcgcTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTAAAAGGGGGGTTTATTAAGGCGTAAATCCCTACAGCATCACATTCCCCTGGCCTCCGAGAAAAAATCGTTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCaga                                                                                           <  2:96168/150‑1 (MQ=255)                                                            gcgagggAAGGTAGGGGGAAAACAGGGGTTATCGGGCGAAAGGGGGGGGTTATTAGGGCGTAAATCCCAACAGCACCACTTTCCCCGGCCCCCCGAAAAAAAACCTCTTTTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAgg                                                                                         <  1:966598/145‑1 (MQ=255)                                                             cgcTGGAAGGTATGGCGCGAACACCGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTCTTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAgggg                                                                                       >  1:1061554/1‑151 (MQ=255)                                                              gcTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGggc                                                                                      >  2:341892/1‑151 (MQ=255)                                                                gggAAGGTAGGGCGAGAACACAGTTTATCTGGCTAAAAGGGGGGGTTATAAAGGCGTAAATCCCTACACCACCACATCCCCCGGCCCCCCGAGAAATAACCGTTTTTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAgg                                                                                         <  2:533408/145‑1 (MQ=255)                                                                     ggTATGGCGAGAACACAGGTTATCTGGCTGAAAGGGGGGTTTATTAAGGCGTGAATCCCTACAGCATCACATTCCCCTGGCCCCCGAGCAATAATCGTTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAgg                                                                                         <  2:111468/141‑1 (MQ=255)                                                                     ggTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCAt                                                                                >  2:577000/1‑150 (MQ=255)                                                                            cGAGAACACATGTTATCTGGTTGACAGAGGGGCCTATTAAGGAGAGAATACCTACAGCATCACATTACGTTGGCCTCAGAGCAATAATCGCGATTACCGCCATAATCGGGGGTGCACGCATGTTTTCGCAGTGTGGCAGGCATATcgc                                                                           >  1:984362/1‑148 (MQ=255)                                                                               aaaCACAGGTTATCTGGCTGAAAGAGGGGTTTTTAAGGGCGTAAATCCCTACACCATCACATTCCCCTGCCCCCGGAGAAAAAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAAc                                                                     <  2:658026/150‑1 (MQ=255)                                                                                aaccggggTTATCGGGTAAAAAGGGGGGTTTTTAAAGGCGTAAATACCACCAGCCCCACATCCCCCTGCCCCCCGAGCAAAAATCGCTATAACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAAc                                                                     <  1:106027/144‑1 (MQ=255)                                                                                   acaGTTTAGCTGGTTAAAAGGGGGGTTTATTAGGGGGTAAACCCCAACAGCCCCCTTTTCCCCGGCCCCCCGGAAAATAACCGTTTTTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTc                                                                  <  1:691104/150‑1 (MQ=255)                                                                                        ttATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCg                                                             >  2:48233/1‑150 (MQ=255)                                                                                          aTCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAAt                                                          >  1:639598/1‑151 (MQ=255)                                                                                            cTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATc                                                         >  2:349562/1‑150 (MQ=255)                                                                                            cTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATc                                                         >  2:197553/1‑150 (MQ=255)                                                                                            cTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATc                                                         >  2:982397/1‑150 (MQ=255)                                                                                              ggCTAAAGGGGGGGTTTATAAGGGGGTAAATCCCTACAGCACCACATTCCCCTCCCCCCCGAGAAATAACCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGaa                                                           <  2:556943/146‑1 (MQ=255)                                                                                                   aaaGGGGGGTTTATAAAGGCGTAAATCCCTACACCATACCATTCCCCTGGCCCCCGAGAAATACCCGTTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTaaaaa                                                 <  2:307924/151‑1 (MQ=255)                                                                                                      ggggggtTTATAAAGGGGTAAATCCCTACACCATCACATTCCCCTGCCCCCCGAAAAATAATCGTTTTTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACg                                               <  2:873376/148‑1 (MQ=255)                                                                                                          gggTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATg                                          >  1:117373/1‑151 (MQ=255)                                                                                                             ttattaTGGCGAAAATCCCTACAAAACCACATTCCCCGGCCCCCCGATAAATATTCTTTTTTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCt                                        <  2:991838/150‑1 (MQ=255)                                                                                                             ttattaAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTg                                       >  2:451305/1‑151 (MQ=255)                                                                                                             ttattaAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTg                                       >  2:927337/1‑151 (MQ=255)                                                                                                                  aaGGCGTAAATCCCTACACCATCACATTCCCCGGCCCCCCGAGAAATAATCGTTATTCCCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGat                                    <  2:143467/149‑1 (MQ=255)                                                                                                                  aaGGCGTAAATCCCCACACCACCACTCCCCCCGGCCCCCCGACCAATACTCGTTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGata                                   <  1:174396/150‑1 (MQ=255)                                                                                                                           acaCCTACAGCATCAAATCCCCCGGCCCCCCGAAAAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCt                            <  2:502842/146‑1 (MQ=255)                                                                                                                                cacacCACCACATGCCCTTGGCCCCCGACTAAAACTCGCTATGTCCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGc                         <  1:455323/145‑1 (MQ=255)                                                                                                                                   aGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCtg                 >  1:415996/1‑151 (MQ=255)                                                                                                                                     cATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCtgtg               >  2:39468/1‑151 (MQ=255)                                                                                                                                        cacaTTCCCCGGGCCCCCGAGAAATAATCGTTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCtgt                <  2:1188080/147‑1 (MQ=255)                                                                                                                                         acaTTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGaaa            >  2:619501/1‑150 (MQ=255)                                                                                                                                                cgtGGCCTCCGACAAAAAACCCGTTTTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGc      <  2:94876/147‑1 (MQ=255)                                                                                                                                                ccTGCCCCCGGAGAAAAAACCTCTTTTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCAt    <  1:39443/151‑1 (MQ=255)                                                                                                                                                 cTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCAtt   >  2:477458/1‑151 (MQ=255)                                                                                                                                                    gCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCATTg  >  2:900589/1‑149 (MQ=255)                                                                                                                                                       |                                                                                                                                                  GCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCGCATTG  >  NC_000913/573253‑573548

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑