Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,504,799	0	A	G	40.8%	71.4 / 15.3	49	G361G (GGA→GGG)	insQ	IS609 transposase B
Reads supporting (aligned to +/- strand):  ref base A (3/26);  new base G (20/0);  total (23/26)
Fisher's exact test for biased strand distribution p-value = 6.26e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACGT  >  NC_000913/1504651‑1504945                                                                                                                                                     |                                                                                                                                                    gggttggggcattcTGTGGTCATAAAGAAAAAGACAACCGCCTGTCACAAATTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGgaga                                                                                                                                                   <  2:343975/138‑1 (MQ=255)             aCTGTGGTAATACAGCAAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAGCGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCa                                                                                                                                          <  2:221313/148‑1 (MQ=255)                 tgGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGGCGCCGGTCTTGCCCGTGGGGGGAAGGGGGAGGCAgg                                                                                                                                    >  1:789610/1‑150 (MQ=255)                        aCAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCCCGCCGTTCTTTCCCGTGGGGAGATGGTGGAGGCAGGGCcccc                                                                                                                              >  2:729294/1‑149 (MQ=255)                          aGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCCGTCTTGCCTGTGGGGGGGTGGGGGAGGCAGGGCGccc                                                                                                                              >  1:162082/1‑147 (MQ=255)                          aGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTTCCTGTGGGGAGATGGGGGAGTCAGGCCGccc                                                                                                                              >  2:862121/1‑147 (MQ=255)                               aaGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCa                                                                                                                     <  2:191144/151‑1 (MQ=255)                                agagACCCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATCCAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCa                                                                                                                     <  2:152257/150‑1 (MQ=255)                                  agaACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGGAGCCGGTCTTGCCTGTGGGGGGATGGGGTGGTGCGGGCGCCCGGTGaaaccgg                                                                                                                   >  1:411875/1‑145 (MQ=255)                                     aCCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCCTTCTTTCCTGTGGGGGGATGGGGCAGTCAGGGCGCCCCGTGGAGCAGG‑aaac                                                                                                              >  2:743287/1‑149 (MQ=255)                                            gTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGaa                                                                                                       <  1:258858/151‑1 (MQ=255)                                            gTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGa                                                                                                        <  2:560719/150‑1 (MQ=255)                                              cacaAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCCGTCTTGCCTGTGGGGAGGTGGGGGAGGCAGGGCGCCCCTTGTAGGAGG‑AAaccacc                                                                                                          >  1:759664/1‑146 (MQ=255)                                                caAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGa                                                                                                   <  2:940979/151‑1 (MQ=255)                                                   aGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCGGTCTTGTCTGTGGGGGGATGGTGCAGTCAGGCCGCCCGTTGTAGCAGG‑AACCCACCGaaa                                                                                                      >  1:238046/1‑145 (MQ=255)                                                       aaTTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGc                                                                                            <  2:624544/151‑1 (MQ=255)                                                        aTTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGAAGCCCCTTTTGCCTGTGGGGGGGAGGGGGAGGCAGGCCCCCCCGTGACGCAGG‑AACCCCCCCCAAAGAtttctgcg                                                                                           >  1:251444/1‑145 (MQ=255)                                                        aTTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGGTCTTGCCTGTGGGGAGATGGGGGAGTCAGGCCGCCCCGTGGAGCAGG‑AACCCACCCAAAAGAttt                                                                                                >  2:388296/1‑145 (MQ=255)                                                           cAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTTCCTGTGGGGAGATGGGGCAGGCCGGCCGCCCCTTGAAGCAGG‑AAACCACCGCAAAGATTTAgggg                                                                                           >  2:154312/1‑146 (MQ=255)                                                           cAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACa                                                                                        <  2:829116/151‑1 (MQ=255)                                                           cAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACa                                                                                        <  1:864643/151‑1 (MQ=255)                                                                 ccAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCGTTCTTTCCCGGGGGGGGAGGGGGGAGGCAGGGCGCCCCCTGGAGCAGG‑GACCCACCGAAAAGAATTAGGGGACAggc                                                                                     >  1:234860/1‑146 (MQ=255)                                                                   aGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAAc                                                                                <  2:514193/151‑1 (MQ=255)                                                                    ggTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCCGTCTTTTTTTTGGGGAGATGGTGCAGAGTGGACCCCCGGCGCAGCAGG‑CAACCACCGCAATAATTTAGGCGagccggcgga                                                                                 >  1:774814/1‑140 (MQ=255)                                                                     gTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCGTTCTTGGCCGTGGGGAGATGGGGCGGTGAGGGCGCCCCGTGAAAGAGG‑AAACCACCGAAAAGATTTAAGCGGCAGGCTgga                                                                                 >  2:383108/1‑146 (MQ=255)                                                                     gTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGt                                                                              <  2:675259/151‑1 (MQ=255)                                                                     gTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGt                                                                              <  1:17190/151‑1 (MQ=255)                                                                       aTGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCCCTCTTGCCCTTGGGGAGGAGGGGCAGGCAGGCCGCCCCTTGAAGCAGG‑AACCCACCGCAAAAATTCAGGCGACAGCCCGAAc                                                                                >  1:919438/1‑147 (MQ=255)                                                                        tgtgGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCCGTCTTTCCCGTGGGGAGATGGGGCAGTCCGGCCGCCCCGTGGAGCAGG‑AAACCCCCGAAATGAATTAGGCGGCAGCCTGAACGTa                                                                             >  2:769357/1‑149 (MQ=255)                                                                           ggATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGGACGCCCGTCTTTCCTGTGGAGGGAAGGGGCAGGCAGGGCCCCCGCTGAAGCAGG‑AAACCCCCCAAAAGATTTAGGGGACAGcccgca                                                                                 >  1:358029/1‑138 (MQ=255)                                                                                taCAGCGAACGCGGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGAt                                                                     <  1:880871/149‑1 (MQ=255)                                                                                taCAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCCTTCTTTCCTGTGGGGAGAGGGGGGAGGCAGGCCGCCCGTTGAAGCAGG‑AAACCACCCAAAAGATTCAGGCGACAGCCCGGACGTAGCAgggggcc                                                                   >  2:155422/1‑147 (MQ=255)                                                                                    gCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGt                                                               <  2:664941/151‑1 (MQ=255)                                                                                    gCGAACGCCGATGTAAATGGCGCACGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGt                                                               <  1:803418/151‑1 (MQ=255)                                                                                          gCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGCTCTTTCCTGTGGGGAGATGGGGGAGTCAGGCCGCCCGCTGAAGCAGG‑AACCCACCCAAAAGATTCAGGCGACAGCCCGAACGTAGCAGGGGGCCACGTCCtt                                                           >  2:85210/1‑149 (MQ=255)                                                                                                   aaTGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTgga                                                <  2:952137/151‑1 (MQ=255)                                                                                                       gcgcTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGAt                                            <  1:297640/151‑1 (MQ=255)                                                                                                       gcgcTCGCAACATTTTAGCGGCGGGGCACGCCCCTCTTTCCTCTGGGGAGAAGGGGGAGTCAGGCCGCCCGCTGTAGCAGG‑AAACCACCCAAATGATTCCGGCGACAGCCCGGACGGAGCAGGGGTGCACGTCCCTCCgggggcggggg                                              >  1:612706/1‑141 (MQ=255)                                                                                                         gcTCGCAACATTTTAGCGGCGGGGCACGCCGCTCCTTTCTGTGGGGAGAAGGTGCAGGCAGACCGCCCCTTGGCGCAGGAAACCCCCCGAAAAAATT‑AGGCGACAGCCCGAAAGGAGAAGGGATCCACCTCCCTCaacgcggggggggag                                           >  1:770846/1‑136 (MQ=255)                                                                                                               aaCATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAata                                     <  1:304041/150‑1 (MQ=255)                                                                                                                aCATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATc                                   <  2:789637/151‑1 (MQ=255)                                                                                                                      tAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGTAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGttt                              <  2:411888/150‑1 (MQ=255)                                                                                                                       aGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGtt                               <  1:774544/148‑1 (MQ=255)                                                                                                                          ggcggGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTc                         >  2:737489/1‑151 (MQ=255)                                                                                                                           gcggGGCCCGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCa                        <  1:939555/151‑1 (MQ=255)                                                                                                                                  aCGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGAtt                  >  2:829210/1‑150 (MQ=255)                                                                                                                                      cGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAAtt             <  1:680427/151‑1 (MQ=255)                                                                                                                                         tCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCa           <  2:536690/150‑1 (MQ=255)                                                                                                                                                 gtgGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACGt  <  1:681874/151‑1 (MQ=255)                                                                                                                                                 gtgGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACGt  <  1:842568/151‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                    AGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGCAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGG‑AACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACGT  >  NC_000913/1504651‑1504945

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑