Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,857,143	0	T	A	46.9%	12.4 / 74.6	49	Y17* (TAT→TAA)	mutS	methyl‑directed mismatch repair protein
Reads supporting (aligned to +/- strand):  ref base T (12/14);  new base A (13/10);  total (25/24)
Fisher's exact test for biased strand distribution p-value = 5.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑AT‑C‑TCAGGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAACTGCTGGATA  >  NC_000913/2857034‑2857249                                                                                                               |                                                                                                             tACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGAt                                                                               >  1:814344/1‑139 (MQ=255)   cAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATcc                                                                             <  2:1217555/139‑1 (MQ=255)     aCGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCctg                                                                           <  1:1571395/139‑1 (MQ=255)      cGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCctgc                                                                          >  1:1699167/1‑139 (MQ=255)       gAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCctgct                                                                         <  2:1699167/139‑1 (MQ=255)                     tCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATgg                                                           >  2:988707/1‑139 (MQ=255)                         acCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGa                                                       <  1:1511330/139‑1 (MQ=255)                             cATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGAtttt                                                   >  1:488797/1‑139 (MQ=255)                              aTTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGAttttt                                                  <  1:988707/139‑1 (MQ=255)                              aTTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGAttttt                                                  <  2:814344/139‑1 (MQ=255)                                ttAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTAt                                                <  1:677707/139‑1 (MQ=255)                                    tatCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                            <  2:488797/139‑1 (MQ=255)                                       cAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGt                                         >  2:271451/1‑139 (MQ=255)                                         gggAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                             <  1:650533/133‑1 (MQ=255)                                         gggAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCctgct                                                                         <  1:75244/105‑1 (MQ=255)                                         gggAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                             >  2:650533/1‑133 (MQ=255)                                         gggAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGG‑GA‑T‑AGTCGCTGAAAGGCCAGCATCCCGAGATCctgct                                                                         >  2:75244/1‑105 (MQ=255)                                              ccGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATga                                  >  1:774015/1‑139 (MQ=255)                                               cGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCg                                                                >  2:1424149/1‑108 (MQ=255)                                               cGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCg                                                                <  1:1424149/108‑1 (MQ=255)                                                 gACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGAT‑AGTC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                             >  1:971270/1‑125 (MQ=255)                                                 gACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                             <  2:971270/125‑1 (MQ=255)                                                      aaCCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGa                                                       <  1:1422645/110‑1 (MQ=255)                                                      aaCCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGa                                                       >  2:1422645/1‑110 (MQ=255)                                                      aaCCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCaa                          >  2:1588669/1‑139 (MQ=255)                                                      aaCCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCaa                          >  2:1234839/1‑139 (MQ=255)                                                           cATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAAcgc                     >  2:1733088/1‑139 (MQ=255)                                                           cATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAAcgc                     >  1:828329/1‑139 (MQ=255)                                                            aTGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                            <  2:111180/115‑1 (MQ=255)                                                            aTGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                            >  1:111180/1‑115 (MQ=255)                                                             tGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCgaga                                                                                >  2:1362564/1‑78 (MQ=255)                                                             tGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCgaga                                                                                <  1:1362564/78‑1 (MQ=255)                                                                gTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAAcg                      <  2:361611/133‑1 (MQ=255)                                                                gTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAAcg                      >  1:361611/1‑133 (MQ=255)                                                                gTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTc                >  2:1470187/1‑139 (MQ=255)                                                                gTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTc                >  1:607019/1‑139 (MQ=255)                                                                   cAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGa                                              >  1:890505/1‑106 (MQ=255)                                                                   cAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGa                                              <  2:890505/106‑1 (MQ=255)                                                                      tAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGA‑TTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAActg         >  2:353360/1‑139 (MQ=255)                                                                      tAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAAct          >  1:807279/1‑139 (MQ=255)                                                                       aGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAActg         <  1:1733088/139‑1 (MQ=255)                                                                       aGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACAGTTTTATTACGAAGCAAAACGCGCGGCGGAAatg         >  2:567860/1‑139 (MQ=255)                                                                        gAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGA‑TTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAActgct       <  1:353360/139‑1 (MQ=255)                                                                         aaaaTTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAActgct       <  1:1470187/139‑1 (MQ=255)                                                                         aaaaTTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAActgct       <  2:774015/139‑1 (MQ=255)                                                                         aaaaTTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAActgct       <  1:271451/139‑1 (MQ=255)                                                                              ttCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAACTGCTGGata  <  2:607019/139‑1 (MQ=255)                                                                                        atacgcccatGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                             <  1:6423/86‑1 (MQ=255)                                                                                        atacgcccatGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                             >  2:6423/1‑86 (MQ=255)                                                                                                               |                                                                                                             TACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑AT‑C‑TCAGGCTGAAAGCCCAGCATCCCGAGATCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAACTGCTGGATA  >  NC_000913/2857034‑2857249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑