Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	56.8%	4.6 / 39.4	37	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (9/7);  new base A (0/21);  total (9/28)
Fisher's exact test for biased strand distribution p-value = 9.20e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.66e-05

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  NC_000913/357741‑358015                                                                                                                                                       |                                                                                                                              tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aac                                                                                                                               >  2:928073/1‑150 (MQ=255)  gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aaca                                                                                                                              <  1:824979/150‑1 (MQ=255)  gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aac                                                                                                                               <  1:345863/149‑1 (MQ=255)     aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAc                                                                                                                          <  1:18606/151‑1 (MQ=255)      aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAcc                                                                                                                         <  2:244464/151‑1 (MQ=255)       gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCCGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAcc                                                                                                                         >  1:942168/1‑150 (MQ=255)         gTAGCGCATCAGGCAATTCCTGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccgcc                                                                                                                      >  1:889348/1‑151 (MQ=255)          tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccgccg                                                                                                                     >  2:55688/1‑151 (MQ=255)                       aaTTCCAGCCGCAGAGCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAACGCCGTTCTCTCCagt                                                                                                          >  1:119241/1‑149 (MQ=255)                          tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                     >  1:833336/1‑151 (MQ=255)                           ccAGCCGCAGCCCTGTGTCAGCGGCTCCCGTGATTCATTCCCGCCAACACCCGCGCATTTACCCACCGCCATGTGCAAAAATGCCTTCGCGGCGGCTTTCTCCCAGCTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                      <  2:12790/149‑1 (MQ=21)                             aGCCGCAGACCTGTGTCAGCGGCTACTGTGGTTCATTTCCGCCAACAACCGCGCATTTATCAAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGGCGC‑AACAAAACCGCCGTGCTCTCGAGTAGTGGCgg                                                                                                  >  1:808498/1‑151 (MQ=21)                              gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                  >  1:475324/1‑150 (MQ=255)                                     cccTGTGCCGGCGCCTACCGTGTTTCATTCCCCCCAACACCCGCCCTTTTATCCACCCCCATGTGCAAAAATCCCTCCGCGGCGGCTCTCTCCCATTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                          <  1:427372/150‑1 (MQ=255)                                          tgccagggacTACGGTGATACTTTCCCGCAAAAACCCGCGCTTTTATCCAACGGCATGTCCAAAATTGCCTTCGGGGCGGCTGTCCGCCGGTTATTTTCCCGCCGA‑AACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                      <  2:363467/141‑1 (MQ=255)                                               gcgcCTACGGTGATTCTTTCCCGCCAACACCCGCGCATTTACCCACCGCCTTGTGAAAAAATGCTTCCGGGGCGGCTTTCTGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                <  2:584613/151‑1 (MQ=255)                                                 gtcTACCGTGATTCTTTCCCCCCAACACCCGCGCATTTACCCAACGCCTTGTGCAAAAATCCCTTCGCGGCGGCTTTCTGCCAGCTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa                                                                                       <  2:713037/140‑1 (MQ=255)                                                  cctcccttaaTTCTTTCCCCCCAACACCCGCGCTTTTCCCCACCGCCATGTGAAAAAATCCCTCCGCGGCGCCTTTCTGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                <  1:726809/139‑1 (MQ=255)                                                   cTACGGTTATTCTTTCCCACAAACACCCGCACTTTTACCAAACCCCTGGTAAAAAAATCCTTCCGCGGCGGTTGTCGCCCAGTTTTTTTCCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg                                                                             <  1:850144/150‑1 (MQ=255)                                                    tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGgaaaaaattttaaac                                                                           >  2:963721/1‑139 (MQ=25)                                                      ccgttttcaaTTCCCCCCACCACCCGCACATTTACCCACCGCAATGTCCAAAATTCCCTCCGCGGCGGCTTTCTCCCAGCTATTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg                                                                             <  2:470988/138‑1 (MQ=255)                                                                      ccAACACCCGCGCTTTTACCCACCGCCTTGTACAAAAATGCCTTCGCGGCGGCTGTCTGCCAGTTTTTTTTCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                          <  2:891928/150‑1 (MQ=255)                                                                             ccGCGCTTTTACCCACCCCCGTTGCCAAAAAGGCTTGCGCGGGGGCTTCCTCCCAGCTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCATCATGTTGTGTGGCAATc                                                       <  1:749897/146‑1 (MQ=255)                                                                              cgcgCATTTACCCACCGCCATGTGCAAAAAGGCCTCCGCGGCGGTTGTCTGCCAGCTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                 <  2:343914/151‑1 (MQ=255)                                                                               gcgcTTTTACCCACCGCAATGTGAAAAAATGCCTTCGCGGCGGCTGTCTGCCGGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGctgctg                                                <  2:736152/151‑1 (MQ=255)                                                                                cgcTTTTACCCAACGCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGctgctg                                                <  2:430683/150‑1 (MQ=255)                                                                                         ccacccccATGTGAAAAAATCCCTCCGCGGCGGCTGTCGGCAAGTTATTTTCCCGCCCC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                        <  2:973080/143‑1 (MQ=255)                                                                                           accGCCATGTCAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                     <  2:252399/148‑1 (MQ=255)                                                                                                       aaaaaTGCTTTCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                        <  2:554164/151‑1 (MQ=255)                                                                                                        aaaaTGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACTTTTAAACCCTCCTGTTGTTTGGGGATCGCCGCTGGTAAAAATATGGGAAGGGGAggggg                       >  2:1002766/1‑147 (MQ=255)                                                                                                         aaaTGCCTCCGCGGCGGCTTTCTGCCAGCTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                      <  2:593834/151‑1 (MQ=255)                                                                                                         aaaGGCTTTCGGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                      <  2:102866/151‑1 (MQ=255)                                                                                                          aaTGCCTCCGGGGCGGCTTTCTGCCAGTTTTTTTCCCCCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                     <  2:132330/151‑1 (MQ=255)                                                                                                                     gggggcTGTCTCCAATTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCt            <  1:835340/146‑1 (MQ=255)                                                                                                                     ggcggtTGTCTCCCGGCTTTTTTCCCGCCCC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGc             <  2:455541/148‑1 (MQ=255)                                                                                                                     ggcggcTGTCTGCCGGCTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTcc          <  2:980493/151‑1 (MQ=255)                                                                                                                               tccaacctttttttCCGCCAC‑AAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAGCcg   <  2:826653/139‑1 (MQ=255)                                                                                                                                 ccAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg   <  1:934882/146‑1 (MQ=255)                                                                                                                                  cAGTTATTTTCCCGCCGC‑AAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc    <  2:511472/144‑1 (MQ=255)                                                                                                                                       ttttttCCCGCGCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc  <  1:615667/141‑1 (MQ=255)                                                                                                                                                       |                                                                                                                              TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  NC_000913/357741‑358015

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑