Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,857,141	1	.	G	50.9%	91.8 / 92.2	53	coding (49/2562 nt)	mutS	methyl‑directed mismatch repair protein
Reads supporting (aligned to +/- strand):  ref base . (16/10);  new base G (13/14);  total (29/24)
Fisher's exact test for biased strand distribution p-value = 4.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GTATCATGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑AT‑C‑TCAGGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAACTGCTGGATATTTCA  >  NC_000913/2857011‑2857254                                                                                                                                    |                                                                                                                     gTATCATGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGtgatagtcg                                                                                                               >  2:1127603/1‑131 (MQ=255)                        tACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑t                                                                                    >  2:1591783/1‑139 (MQ=255)                           aaCGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCct                                                                                 <  1:212355/139‑1 (MQ=255)                                 aaTAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGtt                                                                           >  1:900540/1‑139 (MQ=255)                                          cATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCctgct                                                                              <  2:1571033/127‑1 (MQ=255)                                          cATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCctgct                                                                              >  1:1571033/1‑127 (MQ=255)                                            tCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATgg                                                                >  1:1540159/1‑139 (MQ=255)                                            tCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATgg                                                                >  1:657454/1‑139 (MQ=255)                                             cacaCCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATggg                                                               <  1:1127603/139‑1 (MQ=255)                                                taagatacagatatCAGGGAACCGGACATAACCCCATCAGTGCAATAGAAAACTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTTACATCCCAGCATCCCGATA‑TCCTGCTGTTTTACCGGATGGGTGa                                                            <  1:266692/129‑1 (MQ=255)                                                      tttAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGAT‑AGTC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTa                                                      >  2:78324/1‑139 (MQ=255)                                                      tttAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGATTCCTGCTGTTTTACCGGATGGGTGAttttt                                                       >  1:1749764/1‑139 (MQ=255)                                                          atatCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                                  <  1:1591783/139‑1 (MQ=255)                                                           tatCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGAT‑AGTC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                                 <  2:657454/139‑1 (MQ=255)                                                           tatCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                                 <  2:699844/139‑1 (MQ=255)                                                           tatCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                                 <  1:78324/139‑1 (MQ=255)                                                            atCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCctg                                                                                <  2:1559857/107‑1 (MQ=255)                                                            atCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACt                                                >  1:949114/1‑139 (MQ=255)                                                            atCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACt                                                >  1:651683/1‑139 (MQ=255)                                                            atCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGAT‑AGTC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCctg                                                                                >  1:1559857/1‑107 (MQ=255)                                                              cAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGt                                              >  1:333787/1‑139 (MQ=255)                                                               aGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                                  >  1:1549140/1‑134 (MQ=255)                                                               aGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                                  <  2:1549140/134‑1 (MQ=255)                                                                gggAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGtgatag                                                                                                                  <  1:771834/73‑6 (MQ=255)                                                                gggAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGtgatag                                                                                                                  >  2:771834/1‑68 (MQ=255)                                                                gggAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                                 <  2:922291/134‑1 (MQ=255)                                                                gggAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAc                                                 >  1:922291/1‑134 (MQ=255)                                                                gggAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCctgct                                                                              >  2:1227831/1‑105 (MQ=255)                                                                gggAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCctgct                                                                              <  1:1227831/105‑1 (MQ=255)                                                                gggAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                                  <  1:32462/133‑1 (MQ=255)                                                                gggAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGaa                                                  >  2:32462/1‑133 (MQ=255)                                                                     gcGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAAcctgtctctta                                       >  2:266692/2‑129 (MQ=255)                                                                        gACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATg                                        <  2:781458/135‑1 (MQ=255)                                                                        gACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATg                                        >  1:781458/1‑135 (MQ=255)                                                                                   aTGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAAcgcg                         >  2:412575/1‑139 (MQ=255)                                                                                    tGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCTAAAcgcgc                        >  2:790993/1‑139 (MQ=255)                                                                                       gTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATgac                                      <  1:994015/122‑1 (MQ=255)                                                                                       gTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATgac                                      >  2:994015/1‑122 (MQ=255)                                                                                       gTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTc                     >  1:1499794/1‑139 (MQ=255)                                                                                        tGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATgac                                      >  2:852898/1‑121 (MQ=255)                                                                                        tGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATgac                                      <  1:852898/121‑1 (MQ=255)                                                                                        tGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCg                    >  1:1470875/1‑139 (MQ=255)                                                                                        tGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCg                    >  1:835188/1‑139 (MQ=255)                                                                                        tGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATggg                                                               >  2:597758/1‑96 (MQ=255)                                                                                        tGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATggg                                                               <  1:597758/96‑1 (MQ=255)                                                                                        tGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCg                    >  2:60983/1‑139 (MQ=255)                                                                                         gCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGc                   <  1:790993/139‑1 (MQ=255)                                                                                         gCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGc                   <  2:333787/139‑1 (MQ=255)                                                                                               gAAAATTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGATTCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAActg              <  2:1749764/139‑1 (MQ=255)                                                                                                aaaaTTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAActgct            <  2:1499794/139‑1 (MQ=255)                                                                                                aaaaTTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAActgct            <  2:119062/139‑1 (MQ=255)                                                                                                  aaTTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCctgct                                                                              >  1:653425/1‑71 (MQ=255)                                                                                                  aaTTTCGACGCCCATACGCCCATGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCctgct                                                                              <  2:653425/71‑1 (MQ=255)                                                                                                  aaTTTCGACGCCCATACGCCCATGATGCAGCAGT‑GA‑T‑AGTCGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAACTGCTgg          >  2:879407/1‑139 (MQ=255)                                                                                                          cgcccatacgcccatGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAACTGCTGGATATTTCa  >  2:485047/1‑139 (MQ=255)                                                                                                          cgcccatacgcccatGATGCAGCAGTGATAG‑TC‑‑GCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAACTGCTGGATATTTCa  <  2:1470875/139‑1 (MQ=255)                                                                                                                                    |                                                                                                                     GTATCATGTGCGCCTTATGTGATTACAACGAAAATAAAAACCATCACACCCCATTTAATATCAGGGAACCGGACATAACCCCATGAGTGCAATAGAAAATTTCGACGCCCATACGCCCATGATGCAGCAGT‑AT‑C‑TCAGGCTGAAAGCCCAGCATCCCGAGA‑TCCTGCTGTTTTACCGGATGGGTGATTTTTATGAACTGTTTTATGACGACGCAAAACGCGCGTCGCAACTGCTGGATATTTCA  >  NC_000913/2857011‑2857254

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑