Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,331,790	0	T	G	52.2%	58.4 / 76.9	46	V430G (GTT→GGT)	proP	proline/glycine betaine transporter
Reads supporting (aligned to +/- strand):  ref base T (2/20);  new base G (24/0);  total (26/20)
Fisher's exact test for biased strand distribution p-value = 4.12e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.24e-10

CGCATATCCGTTACAGCGCGCTGGCGGCGGCATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATACAGGAAGCG‑AAGGAAATTCTCGTCGAGCATTACGATAATATCGAGCAGAAAATCGATGATATTGACCA  >  NC_000913/4331646‑4331937                                                                                                                                                  |                                                                                                                                                      cGCATATCCGTTACAGCGCGCTGGCGGCGGCATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGAGGGTGGgtt                                                                                                                                                 >  2:555105/1‑151 (MQ=255)  gCATATCCGTTACAGCGCGCTGGCGGCGGCATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGGGGGTGGgtt                                                                                                                                                 >  1:39397/1‑150 (MQ=255)      atCCGTTACAGCGCGCTGGCGGCGGCATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATc                                                                                                                                             <  1:755623/150‑1 (MQ=255)            tACAGCGCGCTGGCGGCGGCATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGc                                                                                                                                       <  1:519882/150‑1 (MQ=255)                 cgcgcTGGCGGCGGCATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAAcc                                                                                                                                 <  2:586834/151‑1 (MQ=255)                  gcgcTGGCGGCGGCATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGGGGGTGGGTTTAtaaaccgcggga                                                                                                                                   >  1:573524/1‑137 (MQ=255)                    gcTGGCGGCGGCATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGGGGGTGGGTTTATTAACGGCGGAAcc                                                                                                                                 >  2:104498/1‑148 (MQ=255)                       ggcggcggcATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGTGGGTTTATAACCCGCGGAAACATGaa                                                                                                                            >  2:822713/1‑150 (MQ=255)                          ggcggcATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAagag                                                                                                                        <  2:30840/151‑1 (MQ=255)                          ggcggcATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAagag                                                                                                                        <  1:878137/151‑1 (MQ=255)                           gcggcATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGTGGTTTTATTACCCGCGGAACCATGaaa                                                                                                                           >  2:909580/1‑147 (MQ=255)                             ggcATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGTGGGTTTATTACCCGCGGAAACATGAAaga                                                                                                                         >  1:197479/1‑147 (MQ=255)                              gcATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGTGGTTTTATTACCCGCGGAAACAAGAAAAAGACgg                                                                                                                    >  1:803997/1‑151 (MQ=255)                                aTTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGTGGGTTTATTACCCGCGGAAACCTGAAAAAGAAgg                                                                                                                    >  2:114301/1‑149 (MQ=255)                                 tttAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGTGGGTTAATTCCCCGCGGAAACATTAAaga                                                                                                                         >  1:635977/1‑143 (MQ=255)                                 tttAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGGGGGGGGGTTTATTTCCCGCGGAACCCTGAAAAAGAAgg                                                                                                                    >  1:504427/1‑148 (MQ=255)                                      tatTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGTGGGTTTATAAACGGCGGAAACATGaaaaaaaagggcaa                                                                                                                >  1:49601/1‑136 (MQ=255)                                           cGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGtt                                                                                                       <  1:870069/151‑1 (MQ=255)                                           cGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGtt                                                                                                       <  2:377503/151‑1 (MQ=255)                                                    ttGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGTGGGTTTATTACCCGCGTGACCAAGAAAAAAACGGCAAAACGTCCCTTGgaa                                                                                                   >  2:238401/1‑146 (MQ=255)                                                             tGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGTGGTTTTATTACCGGCGGAACCATGAAAAAGAAGGCAAAACGTCCGTTGTAAAGGGCGACA‑cc                                                                                       >  2:9908/1‑148 (MQ=255)                                                             tGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGCGGGTGGTTTTATTAACCGCGGAAACAAGAAAAAGAACGCAAATCGTCCCTTGGAAgggggggcaacg                                                                                       >  2:589118/1‑139 (MQ=255)                                                              gACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑Ccggc                                                                                    <  1:653126/150‑1 (MQ=255)                                                              gACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑Ccggc                                                                                    <  2:732290/150‑1 (MQ=255)                                                                cGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGTGGGTTTATAACCCGCGGGACCCAAAAAAAAACGGCACAACCTCCCTTGTAAAGGGCGACA‑Cccgccg                                                                                  >  1:439648/1‑148 (MQ=255)                                                                   cAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGGGGGTTTATTACCCGCGTAACCATGAAAGAGACGGCCAAACGTCCGTTGGAAGGGGGGGCA‑Ccggcgg                                                                                  >  1:713980/1‑147 (MQ=255)                                                                      cGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGGGGGTGGGTTAATTAACCGCGGAAACATGAAAAAGAAGGGAAAACGTCCGTTGAAAAGGGGGACA‑Accgcgggggca                                                                             >  2:891473/1‑144 (MQ=255)                                                                          ggcggcCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGata                                                                         <  2:514296/149‑1 (MQ=255)                                                                          ggcggcCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGTGGTTTTATTACCCGCGGAAACCTGAAAAAAAAGGCAAAACGTCCGTTGAAAAGGGGGACA‑CCCGCGGCGGCAGa                                                                           >  1:331885/1‑147 (MQ=255)                                                                           gcggcCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATAc                                                                      <  2:32629/151‑1 (MQ=255)                                                                            cggcCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGCGGGGGGTGGGTTTATTAACCGCGGAAACCAT‑AAAGAAAAGGGAAAACGTTCGTTGGAAAGTGGGGCACCcggcggggcaggtaaaa                                                                       >  1:673976/1‑139 (MQ=255)                                                                                         cGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATTACCCGCGGAACCATGAAAAAGACGGCAAAACGTCCGTTGGAAGGGGGGGCA‑CCCGCGGCGGCCGAAAAACAAGGAGCggaag                                                          >  2:278256/1‑145 (MQ=255)                                                                                           aaaGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGTGGTTTAATTACCGGCGGAACCATGAAAGAGAAGGCAAAACGTCCGGTGGAAGGGGCGACA‑CCGGCGGGGGCAGATATACAAGAAGCG‑AAGGaaa                                                      >  2:785203/1‑150 (MQ=255)                                                                                             aGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATACAGGAAGCG‑AAGGAAATtc                                                   <  1:205429/151‑1 (MQ=255)                                                                                                  gCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGGTGGGTTTATCAACCGCGCAAACAAGAAAAAGACGGCAAATCGTCCGTTGAAAGGGGCGACA‑CCCGCGGCGGCCGATATAAAAGAAGCG‑AAGGaaa                                                      >  2:199487/1‑143 (MQ=255)                                                                                                   cAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATACAGGAAGCG‑AAGGAAATTCtcgtcg                                             <  2:916580/151‑1 (MQ=255)                                                                                                            atgatgCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATACAGGAAGCG‑AAGGAAATTCTCGTCGAGCATTACg                                    <  2:504470/151‑1 (MQ=255)                                                                                                               atgCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATACAGGAAGCG‑AAGGAAATTCTCGTCGAGCATTACGata                                 <  1:423099/151‑1 (MQ=255)                                                                                                                     gcctATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATACAGGAAGCG‑AAGGAAATTCTCGTCGAGCATTACGATAATATc                            <  1:41360/150‑1 (MQ=255)                                                                                                                         aTTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATACAGGAAGCG‑AAGGAAATTCTCGTCGAGCATTACGATAATATCGAGc                        <  1:448763/150‑1 (MQ=255)                                                                                                                           tACCTGATGGTAGTGGC‑GGTGGGTGGGTTTATAACCCGCGGGAACCTGAAAGAAAAGGCAAAACGTGCGTTGAAAGGGGGGGGA‑ACCGCGGCGGCAGAGATAAAAGAAGGGAAAGGAAATT‑TCGTCCGGCAATACGataa                                >  1:274294/1‑140 (MQ=255)                                                                                                                                gATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATACAGGAAGCG‑AAGGAAATTCTCGTCGAGCATTACGATAATATCGAGCAGAAAAt                 <  2:724540/150‑1 (MQ=255)                                                                                                                                      aGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATACAGGAAGCG‑AAGGAAATTCTCGTCGAGCATTACGATAATATCGAGCAGAAAATCgatga           <  2:39398/150‑1 (MQ=255)                                                                                                                                      aGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATACAGGAAGCG‑AAGGAAATTCTCGTCGAGCATTACGATAATATCGAGCAGAAAATCgatga           <  1:691261/150‑1 (MQ=255)                                                                                                                                       gTGGC‑GGTGGGTGGTTTAATCACCGGCGTAAACATGAAAAAGACGGCAAAATGTCCGTTGGAAGGTGCGACA‑CCCGCGGGCTCCGATATACAGGAAGCG‑GAGGAAAATTTCGTCCAGCACTAAGATAATATCGAGCAGAAAATCgat             >  1:893127/1‑147 (MQ=255)                                                                                                                                       gTGGC‑GGTGGGTGGTTTAATCACCCGCGTAAACATGAAAAAGACGGCAAATCGTCCGTTGAAAAGGGGGACA‑CCGGCGGCGGCAGAAATAAAAGAAGCG‑AAGGAAAATTTCGTCGAGCATTACGATAATATAGGGCAGAAAAACg               >  1:759084/1‑145 (MQ=255)                                                                                                                                             ggtggtTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATACAGGAAGCG‑AAGGAAATTCTCGTCGAGCATTACGATAATATCGAGCAGAAAATCGATGATATTGAc    <  2:512531/151‑1 (MQ=255)                                                                                                                                                ggttggttTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATACAGGAAGCG‑AAGGAAATTCTCGTCGAGCATTACGATAATATCGAGCAGAAAATCGATGATATTGACCa  <  1:13862/150‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                      CGCATATCCGTTACAGCGCGCTGGCGGCGGCATTTAATATTTCGGTGCTGGTTGCCGGTCTGACGCCAACGCTGGCGGCCTGGCTGGTCGAAAGCTCGCAGAATCTGATGATGCCTGCCTATTACCTGATGGTAGTGGC‑GGTGGTTGGTTTAATCACCGGCGTAACCATGAAAGAGACGGCAAATCGTCCGTTGAAAGGTGCGACA‑CCGGCGGCGTCAGATATACAGGAAGCG‑AAGGAAATTCTCGTCGAGCATTACGATAATATCGAGCAGAAAATCGATGATATTGACCA  >  NC_000913/4331646‑4331937

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑