Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	925,900	0	A	G	43.4%	84.7 / 14.8	53	noncoding (72/88 nt)	serW	tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base A (2/28);  new base G (23/0);  total (25/28)
Fisher's exact test for biased strand distribution p-value = 4.81e-13
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTTCACTGCCGTACAGGCAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑TGGGTGGC‑AACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCAAGAAGAAT  >  NC_000913/925752‑926050                                                                                                                                                       |                                                                                                                                                           aGTTCACTGCCGTACAGGCAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGAtt                                                                                                                                                          <  1:693216/151‑1 (MQ=255)      aCTGTCGTACATGCAGTGTAGAAATTATCAGGTAACATACACCACCCGCTCACCATGTTCACTTCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGT‑GGT‑GAGGGGGGGATTCGAAc                                                                                                                                                     <  2:44302/151‑1 (MQ=25)           cGTACAGGCAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGGTTTTAAacccc                                                                                                                                                 >  2:104266/1‑150 (MQ=255)              aCAGGCAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGTGGGGGGGGGGGTTGGAAcccc                                                                                                                                                  >  2:122843/1‑147 (MQ=255)                  gCAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGtt                                                                                                                                        <  2:629817/151‑1 (MQ=255)                            aaTTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGGTTCGAAACCCCCCA‑ACGTTTCCGtata                                                                                                                                >  1:218869/1‑149 (MQ=25)                             aTTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGGTTTTAAACCCCGAC‑ACCCTGCCGgataaa                                                                                                                              >  2:188142/1‑148 (MQ=25)                             aTTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATa‑cac                                                                                                                            <  1:386020/151‑1 (MQ=255)                                 acaGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACtt                                                                                                                        <  2:730920/151‑1 (MQ=255)                                    ggTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGGGTTGGAACCCCGCT‑ACGtttgcggatatac                                                                                                                             >  2:757389/1‑133 (MQ=25)                                       aaCATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGGTTTGAACCCCCCCT‑ACGTTGCCGTATA‑CACACTTTCCAgg                                                                                                                  >  1:8366/1‑151 (MQ=255)                                       aaCATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAg                                                                                                                   <  2:50595/150‑1 (MQ=255)                                        aCATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGGTTTGAACCCCCGCT‑ACGGTGCCGGATA‑CACACTTTCCCgg                                                                                                                  >  1:563867/1‑150 (MQ=21)                                        aCATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGc                                                                                                                 <  2:549058/151‑1 (MQ=255)                                          aTACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGt                                                                                                               <  1:184502/151‑1 (MQ=255)                                              tCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGGGTCGAACCCCCCAT‑ACGTTGCCGTATA‑CACACCTTCCAGGCGTg                                                                                                              >  1:242467/1‑148 (MQ=255)                                                  cccGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GGGGGGGGGGTTTGAACCCCCCAT‑ACGTTGCCGGATA‑CACACCTTCCAGGCGTGCTcc                                                                                                          >  1:37394/1‑148 (MQ=21)                                                   ccGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCa                                                                                                      <  1:210067/151‑1 (MQ=255)                                                    cGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGA‑GAGGGGGGGGTTCGAACCCCCCCT‑ACGTTTCCGTATA‑CACAATTTCCAgggggggtcc                                                                                                          >  2:81912/1‑138 (MQ=18)                                                          ccaTGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTc                                                                                               <  2:245860/151‑1 (MQ=255)                                                             tGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGGGTCGAACCCCCCAC‑ACGTTTCCGTATA‑AACACTTTTCAGGGGGGGTCCTTCCGCCCCTccg                                                                                             >  1:314687/1‑148 (MQ=18)                                                                 cACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGacac                                                                                         <  1:203496/150‑1 (MQ=255)                                                                  aCTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGGTTCGAAACCCCCCT‑AAGTTGCCGGATA‑AACCCTTTCCCTGCGTGCCCCTTCAGCCCCCCGGCCAccc                                                                                       >  1:478723/1‑150 (MQ=17)                                                                   cTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGA‑GGAGGGGGGATTGGAACCCCCCAT‑ACCGTTTCGTATA‑CACACCTTTCAAGCGTGCTCCTTCCGCCACACGGGCACCTc                                                                                      >  1:377904/1‑151 (MQ=17)                                                                         tACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGGTTCGAACCCCCCCT‑ACGTTTCCGTATA‑CACACTTTTCAGGCGTGCTCCTTCCGCCACTCCGGCACCTCAcc                                                                                   >  1:758450/1‑148 (MQ=17)                                                                          acagacagATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GGGGGGGGGGTTCGAAACCCCGAT‑ACGGTTCCGTATA‑AACACCTTTCCGGCGGGGTCCTTCCGCCCCCCGGGCAccccccccaa                                                                                >  1:717495/1‑142 (MQ=14)                                                                           cagacagaTAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGGG‑GGGGGGGGGGTTGGAACCCCCCA‑‑ACCTTTTGGTTTACCAAACTTTCCCGG‑GGGCTCCTTCACCCACTCGGaccacactc                                                                                    >  1:450403/1‑138 (MQ=9)                                                                              acagaTAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGt                                                                            <  2:418036/150‑1 (MQ=255)                                                                               cagaTAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGGTTCGAACCCCCCAC‑ACGTTGCCGTATA‑CACACTTTTCCGGCGTGCTCCCTCCGCCCCTCCGGCACCCCACCCAATTGttt                                                                          >  1:291570/1‑151 (MQ=14)                                                                                    aaaaTGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCt                                                                      <  1:742555/150‑1 (MQ=255)                                                                                         gCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTTCCaaa                                                                <  1:30250/151‑1 (MQ=255)                                                                                         gCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCaa                                                                 <  1:529013/150‑1 (MQ=255)                                                                                         gCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCaa                                                                 <  2:629339/150‑1 (MQ=255)                                                                                          cGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGGTTCGGACCCCCCCT‑ACGGTGCCGGATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCCCACCCAAATGTTTTTCTACCaaa                                                                >  1:618397/1‑150 (MQ=14)                                                                                           gAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAAcc                                                              <  2:441974/151‑1 (MQ=255)                                                                                                 aaaGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑Tgg                                                       <  1:554869/151‑1 (MQ=255)                                                                                                 aaaGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑Tgg                                                       <  2:551491/151‑1 (MQ=255)                                                                                                              tCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑TGGGTGGC‑AACgggg                                          <  2:450401/150‑1 (MQ=255)                                                                                                                gTACGAGCTCTTCTTTAAATATGGC‑GGT‑GGGGGGGGGGGTCGGAACCCCCCC‑ACCTTTCCGTATA‑AACACTTTTCAGGGGTGGCCCTTTCGCCACCCGGCCACCCCCCCCAAATGTTTTTCTACCCAAACCCA‑TGGGGGGG‑AACgggg                                          >  2:57254/1‑148 (MQ=9)                                                                                                                   cGAGCTCTTCTTTAAATATGGC‑GGT‑GGGGGGGGGGTTCGAAACCCCCGC‑ACGTTTGCCTATA‑CACACCTTCCAGGGGGGCTCCTTTTGCCACCTCGACACCCCACCAAAATTTTTTTCTACCCAAACTCA‑TGGGGGGG‑AAACGGgcg                                        >  2:168862/1‑147 (MQ=2)                                                                                                                     aGCTCTTCTTTAAATATGGC‑GGT‑GAAGGGGGGGTACGGACCCCCCATAACGTTTCC‑TATA‑TAAACTTTCCAGGCGGGGTCCCTCAGCCACCCGCAAACCTCCCCCAAATTTTTTGCTACCCAACCTCC‑TGTGTGGG‑GAAGGGGCGctacc                                   >  2:181355/1‑149 (MQ=9)                                                                                                                      gCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGGGTCGAACCCCCCCT‑ACGTTTCCGGATA‑AACACCTTCCCGGCGGGCTCCCTCAGCCACCCCGACACCCCACCCAAATGTTTTTCTACCAAAACCCC‑TGGGGGGCAAACgggggccac                                     >  1:216833/1‑143 (MQ=9)                                                                                                                         cttcttTAAATATGGC‑GGT‑GAGGGGGGGGTTCGAAACCCCCCT‑ACGTTGCCGCATA‑AACACCTTCCAGGCGGGCTCCTTCAGCCACCCCGGCACCCCACCCAAATTTTTTTCTACCCAACCCCC‑TGGGGGGG‑AACGGGGGGCCACTATAgg                              >  1:186127/1‑151 (MQ=9)                                                                                                                          ttcttTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑TGGGTGGC‑AACGGGGCGCTACtata                                <  1:527844/148‑1 (MQ=255)                                                                                                                           tcttTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑TGGGTGGC‑AACGGGGCGCTACTATAgg                              <  1:344325/149‑1 (MQ=255)                                                                                                                                aaaTATGGC‑GGT‑GAGGGGGGGGTTCGAAACCCCCAT‑ACGTTGTCGTATA‑AACACCTTCCCGGGGTGCTCCCTCAGCCACCCGGACACCCCACCAAAATTTTTTTCTATCAAACCTCATTGGGGGGG‑AAGGGGGGGC‑ACTATAggggggt                         >  2:407080/1‑145 (MQ=9)                                                                                                                                aaaTATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑TGGGTGGC‑AACGGGGCGCTACTATAGGGAGTTg                        <  2:956/150‑1 (MQ=255)                                                                                                                                       gC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑TGGGTGGC‑AACGGGGCGCTACTATAGGGAGTTGGAGTaaaa                <  1:432909/151‑1 (MQ=255)                                                                                                                                              gAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑TGGGTGGC‑AACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTc           >  1:586563/1‑151 (MQ=255)                                                                                                                                              gAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑TGGGTGGC‑AACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTc           <  1:245139/151‑1 (MQ=255)                                                                                                                                               aGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑TGGGTGGC‑AACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCa          <  2:53290/151‑1 (MQ=255)                                                                                                                                               aGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑TGGGTGGC‑AACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCa          <  2:242465/151‑1 (MQ=255)                                                                                                                                                 ggggggATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑TGGGTGGC‑AACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCaag        <  2:280504/151‑1 (MQ=255)                                                                                                                                                       aTTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑TGGGTGGC‑AACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCAAGAAGAAt  >  1:375300/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                           AGTTCACTGCCGTACAGGCAGCTTAGAAATTCACAGGTAACATACTCCACCCGCCCACCATGTTCACTGCCGTACAGACAGATAAAATGCGAAAAAAAAGCTCGCACTTTCGTACGAGCTCTTCTTTAAATATGGC‑GGT‑GAGGGGGGGATTCGAACCCCCGAT‑ACGTTGCCGTATA‑CACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTTTTGCTACCAAACCTCA‑TGGGTGGC‑AACGGGGCGCTACTATAGGGAGTTGGAGTAAAACGGTCAAGAAGAAT  >  NC_000913/925752‑926050

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑