Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	345,328	0	C	A	55.0%	23.0 / 66.4	40	intergenic (+337/‑76)	yahL/yahM	uncharacterized protein/uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base C (15/3);  new base A (0/22);  total (15/25)
Fisher's exact test for biased strand distribution p-value = 2.03e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.34e-06

AATGATCTCATGCAGATGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCC‑ATCATGTTTGTGTGGGGTCTTTTCT‑G‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTATCATCCCTGCAAAGTGGAACAT  >  NC_000913/345183‑345473                                                                                                                                                     |                                                                                                                                                  aaTGATCTCATGCAGATGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCC‑ATCATGTTTGTGTGGGGTCTTTTCT‑G‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCaaaaa                                                                                                                                              <  1:104949/151‑1 (MQ=255)     aTCTCATGCAGATGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCC‑ATCATGTTTGTGTGGGGTCTTTTCT‑G‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCg                                                                                                                                           >  2:52784/1‑150 (MQ=255)             aagttGTTTTGTGAATGTGTTGGTTGACATTCATATAAAAAAAATCATAATCCC‑ATCATGTTTGTGTGGGGTTTTTTCT‑G‑TATCTTACGCACCGCACTCAACCCTGAAAGAAAATATGCTGTAAGGCTCATATAAAAAACCGCCATTAGCt                                                                                                                                  <  1:367349/147‑1 (MQ=255)               gATGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCC‑ATCATGTTTGTGTGGGGTCTTTTCT‑G‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCtca                                                                                                                                >  1:191993/1‑151 (MQ=255)                atttttgGTGAATGTGTTGGTTGACATTCATATAAAAAAAATAATAATCCC‑ATAATTTTTGTGTGGGGTCTTTTTT‑G‑TATCTTACCCACCGCACCAAACCCTGACAAAAAATATGCTTTAAGCCTCATATAAAAAACCGCCATTAGCt                                                                                                                                  <  1:377464/145‑1 (MQ=255)                 tGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCC‑ATCATGTTTGTGTGGGGTCTTTTCT‑G‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCtcat                                                                                                                               >  1:10363/1‑150 (MQ=255)                     ttGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCC‑ATCATGTTTGTGTGGGGTCTTTTCT‑G‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGa                                                                                                                          >  1:167292/1‑151 (MQ=255)                        taaaTGTGTTGGTGGACTTTCATATGAAAAAAATAATAATCCC‑ATCATTTTTGTGTGGGTTTTTTTCT‑G‑TATCTTACGCACCCCACTCAACCCTGACAAAAAATATGCTGAAAGGCTCATAAAAAAAACCGCCATTAGCTCATCAGGAag                                                                                                                        <  2:347195/148‑1 (MQ=255)                           aTGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCC‑ATCATGTTTGTGTGGGGTCTTTTCT‑G‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCa                                                                                                                    >  2:142940/1‑151 (MQ=255)                               gttggttgACATTCATATGAAAAAAATCATAATTCC‑ATCATGTTTGTGTGGGGGCTTTTCT‑G‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAgacg                                                                                                                >  2:273992/1‑151 (MQ=255)                                    tttaCATTAATATAAAAAAAACCAAAATCCC‑ATCATGTTTG‑GGGGGGTTTTTTTT‑GTTATCTTCCGCATCCCACCCAGCCCTGAAAAAAAATATGCTTTAAGCCTCAAATAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAAc                                                                                                           <  2:290831/148‑1 (MQ=255)                                               ataaaaaaaaTCTAAATAAC‑ATTTTTTTGGTGTGTGTTTTTTTTT‑T‑TATCTTACTCATCCCACTCAACCCTAACAGAAAATTGGTTGGAAGGCTCAATTCAAAATCCGCCATTAGCTCATCAGGAAGAGCAGACGACACCCAGGAttgttg                                                                                                <  2:187550/148‑1 (MQ=255)                                               atGAAAAAAATCATAATCCC‑ATCATGTTTGTGTGGGTTTTTTTCT‑G‑TATCTTCCGCACCGCACTCACGCCTACAAAAAAATATGCTGAAGGGCTCATAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAttgttg                                                                                                <  1:340630/151‑1 (MQ=255)                                               aaaaaaaaaaCCATAATCCC‑ATCATGTTTGGGTGGGTTTTTTTCT‑T‑TATCTTACGCATCGCCCTCAAGCCTGAAAAAAAATATGCTGAAAGCCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAttgttg                                                                                                <  1:119056/148‑1 (MQ=255)                                                  aaaaaaaTCAAATTCCC‑ATCATGTTTGTGTGGGGTTTTTCCT‑G‑TATTTTACGCATCGAACACAACCTTAAAAAAAAATATGCTGAAGGCCTCATAAAAAAAGCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTAt                                                                                             <  1:16566/151‑1 (MQ=255)                                                    aaaaataaaaatCCC‑ATAATGTTTGTGGGGGGTTTTTTCT‑T‑TATTTTCCCCACCGCCCCCAAGCCTAAAAAAAAATATGCGGTAAGGCTCATATAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATgg                                                                                           <  2:227698/151‑1 (MQ=255)                                                    aaaaaaaaaactccc‑ATCTTTTTTGTGGGGGGTTTTTTCT‑G‑AATCTTCCCCACCCCCCCCAACCCAAAAAAAAAATAGGCGGTAAGACCAAAAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATgg                                                                                           <  2:16683/138‑1 (MQ=255)                                                    aaaaaTCATATTCCC‑AAGA‑GTTTTTTTGGGGTTCTTTCTGG‑GATCTTCCCCATCGCATCAAAGCCGAAAAAAAAATATGTTGTAGGGTTAAAAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATgg                                                                                           <  1:252942/151‑1 (MQ=255)                                                    aaaaaTCAAAATCCC‑ATCTTTTTTGTGGGGGTTTTTTTTT‑G‑TATCTTCCGCACCGCCCACAGGCCTAAAAAAAAAAAGGCTGAAAGGCTAATTTAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATgg                                                                                           <  2:260822/151‑1 (MQ=255)                                                         tCAAAATCCC‑ATATTTTTTGTTTGGGGTTTTTTCT‑T‑TATCTAACCCCTCGCCCTCAACCCGGAAAGAAAATATACTTTAAGCCTAATATAAAAATCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACgg                                                                                      <  2:333754/151‑1 (MQ=255)                                                            aaaTCCC‑ATATTGTTGTTGTGGTGTTTTTTTT‑G‑TTTCTCACGAATCACACTCAACCTTTAAAAAAAATTTGCTGAAAGCCTAATCAAAAAATCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGt                                                                                   <  2:354184/150‑1 (MQ=255)                                                             aaTTCCAATCATTTTTGTGGGGGTTTTTTTTT‑T‑TTTTTTCCCCACCGCACCCAACCTTGACAAAAAATATGTTAAAGGCCTCAAATAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGt                                                                                   <  1:174680/151‑1 (MQ=255)                                                                 cc‑ATCATGTTTGTGTGGGTTTTTTTTT‑G‑TATCTTCCGCATCGCACTAAAGCCTGAAAAAAAATATGCTGAAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAg                                                                              <  1:190612/151‑1 (MQ=255)                                                                       atGTTTGTGTGGGGTCTTTTCT‑G‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCt                                                                          >  1:241815/1‑150 (MQ=255)                                                                             gggtgGGTTTTTTTTT‑T‑TATCTTACGCACCGCCCCCAACCCGGAAAAAAAATATGCTGAAGGCCTAAAAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATgg                                                                    <  1:393098/148‑1 (MQ=255)                                                                              tgtgGGGTTTTTTCT‑G‑TATCTTACGAACCGCACCAAGGCCTGACAAAAAATATGCTGAAGGGCTCATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGcc                                                                  <  1:156281/151‑2 (MQ=255)                                                                                  gggTCTTTTCT‑G‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTc                                                               >  2:387782/1‑150 (MQ=255)                                                                                    gTCTTTTCT‑G‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCaa                                                            >  2:10924/1‑151 (MQ=255)                                                                                        tttCT‑G‑TATCTTACTCATCGCACTCAAGCCTGACAGCAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGCTGCATGGAACGGGGTTCGAGGCCTCGATGGCGGTCTCACttt                                                        >  1:55437/1‑151 (MQ=255)                                                                                        tttCT‑G‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACttt                                                        >  1:160886/1‑151 (MQ=255)                                                                                              g‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCaaa                                                   >  2:74160/1‑151 (MQ=255)                                                                                                         caccccACTAAACCCTTAAAAAAAATATTCGGTAGGGCTAAAACAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGa                                         <  2:286359/146‑1 (MQ=255)                                                                                                           cccccctaaaGCCTGAAAGAAAATATGCTATAAGCCTCATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAAt                                       <  2:326327/143‑1 (MQ=255)                                                                                                           ccGCACACAAGCCTAACAAAAAATATGCAGAAAGGCTAAAATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAAt                                       <  1:182581/150‑1 (MQ=255)                                                                                                              cACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAg                                    >  2:45716/1‑151 (MQ=255)                                                                                                                           aaaaaaaTATCCTAAAAGCCTAATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTtattat                       <  2:179088/148‑1 (MQ=255)                                                                                                                               aaaTATGCTGAAAGCCTAAAATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTatcatc                   <  2:84773/151‑1 (MQ=255)                                                                                                                                      cTGAAAGGCCAAAATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTATCATCCCTGCaa            <  2:78878/151‑1 (MQ=255)                                                                                                                                            ggCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTATCATCCCTGCAAAGTGGa      >  2:124995/1‑151 (MQ=255)                                                                                                                                                cATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTATCATCCCTGCAAAGTGGAACAt  >  2:145198/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                  AATGATCTCATGCAGATGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCC‑ATCATGTTTGTGTGGGGTCTTTTCT‑G‑TATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTATCATCCCTGCAAAGTGGAACAT  >  NC_000913/345183‑345473

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑