Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,730	0	C	A	42.9%	63.3 / 20.9	42	N310K (AAC→AAA)	thrB	homoserine kinase
Reads supporting (aligned to +/- strand):  ref base C (9/15);  new base A (18/0);  total (27/15)
Fisher's exact test for biased strand distribution p-value = 1.40e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGC  >  NC_000913/3581‑3872                                                                                                                                                      |                                                                                                                                                   ggctccggcCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACt                                                                                                                                                   <  1:422200/151‑1 (MQ=255)     ccggcCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTaaa                                                                                                                                                <  1:266361/150‑1 (MQ=255)          ccGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGGGCACGGGGACTGGGAAACaaaaaaaaa                                                                                                                                           >  1:39197/1‑145 (MQ=255)          ccGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCCAGAGGAATGGGAAAATAAATTaaa                                                                                                                                           >  2:131624/1‑150 (MQ=255)             aCCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAActct                                                                                                                                       <  1:328234/151‑1 (MQ=255)                 tGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCCCGGGGAGTGGGAAACaaaaaaaaa                                                                                                                                           >  1:474928/1‑138 (MQ=255)                      gCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGa                                                                                                                              <  2:624917/151‑1 (MQ=255)                                aCAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATcaca                                                                                                                     <  1:494683/150‑1 (MQ=255)                                      cGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCa                                                                                                              <  2:874268/151‑1 (MQ=255)                                          aaCCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGGGCCCCAGGAATGGGGAAATAAAAAAAAAACTACAAACTGAAAGAACACaa                                                                                                                    >  1:97102/1‑141 (MQ=255)                                                ccAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGGACTGGGAAAATAAATGAAAATCTACAAACTGAAAAAACACAACAAGCAGGGCAGCttt                                                                                                    >  2:515186/1‑151 (MQ=255)                                                ccAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTGGCCGGCTGGATACGGCGGGCGCACGAGGACTGGAAAAATAAATGAAAATCTACAAACTTAAAGAACACAACGAACAGGGCAGCttt                                                                                                    >  2:547592/1‑151 (MQ=255)                                                                tGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCCCGAGGACTGGGAAAATAAAAAAAAATCTTCAATCTGAAAGAACACAAACAGCAAGGCAGCCTTTC‑GCAAGACGT‑TAccc                                                                                  >  1:887529/1‑151 (MQ=255)                                                                  gTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACCAGGCCTGGAAAAACAAAAGAAAAATTAAAATCTTAAAGAACACAACAAACAGGTCCGCCTTTC‑GCcaacccc‑aaccc                                                                                  >  1:749794/1‑149 (MQ=255)                                                                     gggTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGGGCACGAGGAATTGGAAAATAAAAGAAAATCTACAATCTTTAAAATCAAAAAGAGCAGGGCAGGTTTTT‑GCAAGCCGT‑AAACC‑A‑gggg                                                                           >  2:583983/1‑151 (MQ=255)                                                                     gggTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑gggg                                                                           <  1:286191/151‑1 (MQ=255)                                                                        tAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGGACGAGAAATGGGAAAATAAATGAAAATATAAAAACTGAAAAAAAAAAACAAGCCAGGCAGCTTTTC‑GCAAGCCGTAAACCC‑A‑ggg                                                                            >  2:631185/1‑148 (MQ=255)                                                                           gAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCCCGAGGACTGGAAAAATAAATGAAACTCTACAAACTTAAAGATAACAACAAGCAGGTCAGCTTTGT‑GCCAGCCGT‑AACCC‑A‑GGGGGTggg                                                                      >  1:419037/1‑150 (MQ=255)                                                                                     cAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGGACTGGGAAAATAAATGAAAATCTACAAACTTAAAGAACACCACGAGCAGGTCAGCTTTTC‑GCAAACCGT‑AAACC‑C‑GGGGGTGGGGaaaaaatagg                                                           >  2:255491/1‑146 (MQ=255)                                                                                      aaaaTCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCCCGGGTACTGGGAAAATAAATGAAACACTTCAAACTGAAAAAACACAACGAGCAGGGCCGCTTTGC‑GGAAGCCGT‑AACCC‑C‑AGGGGTGGGGAAAAAACAggg                                                          >  2:638809/1‑151 (MQ=255)                                                                                       aaaTCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGGACGAGGACTGGGAAAATAAATTAAAATTTACAAACTTAAAGAATAAAAAGAGCAGGGCAGATTTTC‑GCAAGGCGT‑AAACC‑ACGGGGTTGGGGAAAAACAAggg                                                          >  2:689641/1‑151 (MQ=255)                                                                                        aaTCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGc                                                        <  1:604888/151‑1 (MQ=255)                                                                                         aTCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGGGCACGAGGACTGGAAAAATAAAAGAAAATCTACAATCTTAAAGAACACAACGAGCAGGTCAGGTTTTG‑GCAAAGCCT‑AACCC‑A‑GGGGGTGGGGaaaaaaaaaggggt                                                       >  2:312157/1‑142 (MQ=255)                                                                                             ggAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGttt                                                   <  1:186022/151‑1 (MQ=255)                                                                                                    tttGTTCATATTTGCCGGCTGGATACGGCGGGCGCCCCGGTACTTGGAAAAAAAATGAAAATCTACAATCTTAAAGATCACAACGAGAAGGGCAGCCTTTC‑GCAAACCGT‑AACCC‑A‑GGGGGTGGGCAAAAAAAAGGGGGTGtttttt                                                >  1:287204/1‑147 (MQ=255)                                                                                                    tttGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGGTCTGTGAAAAAAAAAAAAAATCTACAATCTGAAAGATTACAACGAACAGGGCAGAGTTGC‑GCAAGCCCT‑AAACC‑ACGGGGGGGGGAAAAAAAAAGGGGGGGtttttt                                                >  1:298735/1‑148 (MQ=255)                                                                                                       gTTCATATTTGCCGGCTGGATACGGCGGGCGGCAGGGGACCGGAAAAATTAATTAAACACTTCAATACTAAAGGACACAAACAGCAAGGCCGCCTTGCGGCAACCCTC‑ACCCC‑C‑GGGGTTGGGCAAAAATCGGGGGTGGTTTTTTcgc                                             >  1:230480/1‑146 (MQ=255)                                                                                                       gTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCAc                                          <  1:159582/150‑1 (MQ=255)                                                                                                       gTTCATATTTGCCGGCTGGATACGGCGGCCGCACGAGTACTTGGTAACTAAATATAACATTTAACTCTGTAAGGTCACAACAAGCAGGTCAGAATTTC‑GCTACCCCT‑CACCCAA‑CGGATGGGGGAAAAAACAGGGCGTTTTTTTTcccccc                                          >  2:769703/1‑147 (MQ=255)                                                                                                        ttCATATTTGCCGGCTGGATACGGCGGGGGGACGGGGAATGGGAAAATAAATTAAAATCTAAAAAATGAAAGAAAAAAAAGAGGAGGGCAGATTTTT‑GCAAAGCGT‑AAAAC‑A‑GGGGGTGGGGGAAAAAAAAGGGGGGttttttttgcggg                                         >  1:25211/1‑143 (MQ=255)                                                                                                          cATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGAc                                       <  2:812396/150‑1 (MQ=255)                                                                                                          cATATTTGCCGGCTGGATACGGCGGGCGCACGAGGACTGGGAAAATAAAAGAAAATCTACAATCTGAAAAAACACAACGAGCAGGGCAGCTTTTT‑GCAAACCGT‑AACCC‑C‑GGGGGTGGGGAAAAAAAAGGGGGTGTTTTTTTCGCAc                                          >  2:842333/1‑147 (MQ=255)                                                                                                          cATAGTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑TCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGAc                                       <  1:702758/150‑1 (MQ=255)                                                                                                           atatTTGCCGGCTGGATACGGCGGGCGCACGAGGAACGGAAAACTAAAAGAAAATTTACAAACTGAAAGAACACAACAAGCCAGGCAGCCTTGC‑GCAAGCCGT‑AAACC‑C‑GGGGGTGGGGAAAAAACAGGGGGGGTTTTTTTCTCCCGAcc                                      >  2:702980/1‑150 (MQ=255)                                                                                                                   cGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAAt                             <  2:876274/151‑1 (MQ=255)                                                                                                                        ggATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGc                        <  2:816697/151‑1 (MQ=255)                                                                                                                          aTACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGcc                       <  1:440996/150‑1 (MQ=255)                                                                                                                              ggcgggcgCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCctgact                  >  2:392579/1‑151 (MQ=255)                                                                                                                                     gcACGAGTACTGGAAAACTAAATGAACCTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATtg           >  1:266935/1‑151 (MQ=255)                                                                                                                                       aCGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATtgat         >  2:219398/1‑151 (MQ=255)                                                                                                                                         gAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATtgatg        >  2:772438/1‑150 (MQ=255)                                                                                                                                              cTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGc  >  1:575057/1‑151 (MQ=255)                                                                                                                                                      |                                                                                                                                                   GGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC‑GCAAGCCGT‑AACCC‑A‑GGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGC  >  NC_000913/3581‑3872

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑