Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,504,799	0	A	G	42.3%	75.0 / 18.5	53	G361G (GGA→GGG)	insQ	IS609 transposase B
Reads supporting (aligned to +/- strand):  ref base A (2/28);  new base G (22/0);  total (25/28)
Fisher's exact test for biased strand distribution p-value = 1.02e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACG  >  NC_000913/1504658‑1504944                                                                                                                                               |                                                                                                                                                     cgcgTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCCCTC‑TTTCCTGTGGAGAGATgggg                                                                                                                                             >  1:55986/1‑149 (MQ=255)      aCTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGGTT‑TTGTCTGTGGGGGGGTGGTGCAGt                                                                                                                                         >  1:215750/1‑150 (MQ=255)                   aGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCGCTC‑TTGCCTGTGGGGAGATGGGGGAGGCAGGCCGccc                                                                                                                               >  2:1107433/1‑147 (MQ=255)                     cGAAAAAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGACCGCCGATGTAAATGGGGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGtt                                                                                                                            <  2:898541/148‑1 (MQ=255)                        aaGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCa                                                                                                                      <  2:704201/151‑1 (MQ=255)                          gagaACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGGTC‑TTTCCTGTGGGGAGAAGGTGGAGTCAGGGCcccc                                                                                                                               >  1:76739/1‑140 (MQ=255)                                cGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTTCCTGTGGGGGGATGGTGGAGTCAGGCCGCCCCTTGAAGCA‑GGAAacc                                                                                                              >  2:1134110/1‑150 (MQ=255)                                         caAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGGCGCCCTTC‑TTTCCCGTGGGGGGAAGGGGGGGGCAGGCCGCCCCCTGGAGCA‑GGAACCCC‑CCCaaa                                                                                                      >  1:845567/1‑148 (MQ=255)                                         caAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCCCTCCGGTC‑TTGCATGGCGGAAGGTGGTGGAGATGAGCCGCCCCTCGTAGTA‑GGGAACCA‑CCGaaa                                                                                                      >  1:462380/1‑148 (MQ=255)                                                aaTTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCGGTC‑TTGCCTGTGGGGAGATGGGGGAGGGAGGGCGCCCGCTGAAGCA‑AGAAACCA‑CCCAAAAGAtttaag                                                                                             >  1:178113/1‑146 (MQ=255)                                                 aTTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCg                                                                                           <  2:75965/151‑1 (MQ=255)                                                  ttCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACCCCGGTCTTTTCCTTTGG‑GGGAAGGGGCAGCAAGGCCGCCCCGTGAAGCAGGGAAcccc‑cccacagattccagcg                                                                                            >  1:1027572/1‑136 (MQ=255)                                                       aTGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑Gcc                                                                                    <  1:1071928/151‑1 (MQ=255)                                                       aTGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCCCTC‑TTGCCTGTGGGGAGATGGGGGAGGCAAGCCGCCCCGTGAAGAA‑GGAAACCA‑ACCAAAAGATTCAAGCGACA‑ggc                                                                                    >  2:991754/1‑149 (MQ=255)                                                         gCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCt                                                                                   <  1:794168/150‑1 (MQ=255)                                                            aGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAAc                                                                               <  2:978800/151‑1 (MQ=255)                                                             ggTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGCCGCCCGTC‑TTTTCTGTGGGGAGAAGGGGGCGGGAGGGCCCCCCGTGAAGCA‑GGAAACCC‑CCCCAAAGATTTAAGCGACaagccgga                                                                                 >  1:1015445/1‑142 (MQ=255)                                                              gTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGt                                                                             <  2:49521/151‑1 (MQ=255)                                                                 tgtgGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGGTT‑TTTCCTGTGGGGAGAGGGGGGAGGCAGGGCGCCCGCTGGAGCA‑GGAACCCA‑CCGAAAAGATTCAGGCGACC‑Gcc                                                                                    >  1:1140297/1‑141 (MQ=255)                                                                  gtgGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGc                                                                          <  1:932579/150‑1 (MQ=255)                                                                   tgGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCGGTC‑TTTCCTGTGGGGGGAAGGGGGAGTCAGGCCCCCCGCTGAAGCA‑CGGAACCA‑CCCAAAAGATTTACGCGAAA‑ACCTGGACGTaac                                                                          >  1:34673/1‑147 (MQ=255)                                                                    ggATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCGGTT‑TTTCCTGTGGGGAGGTGGTGCAGGCAGGCCGCCCCCTGTAACA‑GGAAGCCA‑CCGAAAAGATTTAGGGGGCA‑GCCTGAAACGAGCAgg                                                                       >  2:644468/1‑151 (MQ=255)                                                                     gATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCCCTC‑TTTCCTGTGGGGAGAAGGGGGAGGCAGGGCCGCCGCTTAAGCA‑GGAAGCCACCCGAAAGAATTTA‑GCCAAA‑GCCTCCACATAGCAggg                                                                      >  2:214990/1‑151 (MQ=255)                                                                        ataCAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCGCTC‑TTTTCCGTGGGGAGAGGGGGCCGGCAGGCCGCCCGGTGAAGCA‑GGAACCCC‑CCGAAAAGAATCAAGGGACA‑GCCCGAACGTAGCAggggac                                                                   >  2:1154261/1‑148 (MQ=255)                                                                         taCAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCCGTC‑TTGTCCGTGGGGAGAGGGGGCCGGCAGGGCGCCCCTTGGAGCA‑GGAAACCC‑CCCAAAAGATTCAGGCGAAACACCTG‑ACGTAGCAGGGGTcc                                                                  >  1:862565/1‑151 (MQ=255)                                                                             gCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTTCCTGTGGGGAGAAGGGGCCGGCAAGCCCCCCGTTTGAGCA‑GGGAACCC‑CCCCAATGATTTAAGCGACC‑ACCCGAACCGAGCAAGGGTCCACGt                                                              >  2:600307/1‑151 (MQ=255)                                                                                  cGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTc                                                         <  1:931038/151‑1 (MQ=255)                                                                                   gCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCCTTC‑TTTCCTGTGGGGAGATGGGGCGGTCAGGCCCCCCGCTGAAGCA‑GGAACCCC‑CCGCAAAGATTTAGGCGACA‑GCCCGAACGGAGCAGGGGTCCACGTcc                                                            >  2:303680/1‑147 (MQ=255)                                                                                         gTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGt                                                  <  1:1100036/151‑1 (MQ=255)                                                                                          tAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGGCCGTC‑TTTGCTGTGGGGGGATGGTGGAGTCAGGCCGCCCGTTGAAGCA‑GGGACCCA‑CCCAAAAGATTTAGGCGGCA‑GCCCGAACGGAGCAGGGATCCACCTCCTTCAGGGCggg                                                 >  1:698450/1‑149 (MQ=255)                                                                                              tGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTTCCCGTGGGGAGATGGTGCAGTCAGGCCGCCCCTTGAAGCA‑GGAACCCA‑CCCAAAAGATTTAGGCGACA‑GCCCGAAAGTAGGAGGGGTCCACGTCCTTCCggggggggggg                                             >  2:30080/1‑143 (MQ=255)                                                                                                gcgcTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGAt                                           <  1:11984/151‑1 (MQ=255)                                                                                                gcgcTCGCAACATTTTAGCGGCGGGGCACGCCCTTC‑TTTCCTTTGGGGAGAGGGGGCAGTCAGGCCGCCCCTTGGAGCA‑GGAACCCA‑CCCAAAAGATTTAAGCGACC‑GCCTGAACGTAGCAGGGGTCCACGCCCTTCCGGGCGgggggg                                             >  2:705617/1‑149 (MQ=255)                                                                                                  gcTCGCAACATTTTAGCGGCGGGGCACGCCCGTC‑TTGCCTGCGGGGGGATGGTGGAGGCCGGGCGCCCGTTGGAGGA‑GGGACCCA‑CCCAAAAGATTTTGGCGGCA‑GCCCGGACGGAGCCGGGGTCCCCGTCCTTCCggggggggggg                                             >  1:389314/1‑139 (MQ=255)                                                                                                     cGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTc                                        <  1:563349/149‑1 (MQ=255)                                                                                                     cGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCa                                       <  2:447349/150‑1 (MQ=255)                                                                                                        aaCATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAatat                                   <  2:641806/151‑1 (MQ=255)                                                                                                          cATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGAGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCg                                 <  2:784945/151‑1 (MQ=255)                                                                                                               tAGCGGCGGGGGACGCCGTTT‑TTGTCTGTGGGGAGATGGGGCGGTGAGGGCGCCCGTTGAAGCA‑GGAAACCC‑CCGAAATGATTCAGGCGACA‑GCCTGAACGGAGCAGGGGTCCACGGCCTTCAGGGCGGGGAGGATGTCAATATCGGttt                             >  1:123107/1‑150 (MQ=255)                                                                                                               tAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGttt                             <  1:390887/150‑1 (MQ=255)                                                                                                               tAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGttt                             <  2:985058/150‑1 (MQ=255)                                                                                                                aGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTc                            <  1:37594/150‑1 (MQ=255)                                                                                                                aGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCt                           <  2:611233/151‑1 (MQ=255)                                                                                                                 gcggcgGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTg                          <  2:839878/151‑1 (MQ=255)                                                                                                                  cggcggGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCt                           >  1:435219/1‑149 (MQ=255)                                                                                                                  cggcggGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGt                         <  2:597783/151‑1 (MQ=255)                                                                                                                   ggcggGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGt                         <  1:483452/150‑1 (MQ=255)                                                                                                                   ggcggGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTc                        <  1:847731/151‑1 (MQ=255)                                                                                                                      ggggCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGc                     <  1:154622/151‑1 (MQ=255)                                                                                                                          cACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAGCGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGAt                  <  1:885403/150‑1 (MQ=255)                                                                                                                             gCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTaaa              <  1:128079/151‑1 (MQ=255)                                                                                                                                      tGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAaca       <  2:259320/150‑1 (MQ=255)                                                                                                                                           gtgGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACg  <  2:529333/150‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                     CGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTC‑TTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCA‑GGAACCCA‑CCGAAATGATTCAGGCGACA‑GCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACG  >  NC_000913/1504658‑1504944

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑