Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	295,230	1	.	T	60.9%	47.1 / 11.6	23	coding (350/441 nt)	yagN	CP4‑6 prophage; protein YagN
Reads supporting (aligned to +/- strand):  ref base . (7/2);  new base T (14/0);  total (21/2)
Fisher's exact test for biased strand distribution p-value = 1.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.55e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGAATGG‑TTTGAGA‑TTTGTAGCTAA‑TGA‑TTTTAGCTAACTCAGCTG‑TTGAAATGAGCTGTGA‑TTGAGATGTATCC‑GGGAG‑TTTGAATGC‑GCTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACG‑TTTC‑GGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGTG‑ATGCGATCTGGATGCCTGA‑TTTTTACATGACATCA‑GACGCG‑CGAGAAA‑GTT‑AGTAGCATTTTGCATTC‑TTTG‑TTTAAGATGTAAAATTTTCA‑G‑TTTGGCGCATGCG‑ACAGAC‑TTGCGAAGAGCTGAGTATGTTCCTTTGAGATACTCGACAACCTCTTCCATGGACGCAGGATCGTTAAAGGATTGAG  >  NC_000913/294993‑295497                                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                                                            gATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGAATGGTTTTGAGA‑‑TTGTAGCTAA‑TGA‑TTTTAGCTAACTCAGCTG‑TTGAAATGAGCTGTGA‑TTGAGATGTATCC‑GGGAG‑TTTGAATGC‑GCTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACGTTTTC‑GGGCTCGGGGTC‑GGGGTCACTACCGATCACCTGAATCTGATGATAA‑GCAC‑TTTTAGCTGA‑TTAGCCGTACTGTG‑ATGCGATCTGGAt                                                                                                                                                                                            >  1:375999/1‑330 (MQ=255)        tttGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGAATGG‑TTTGAGA‑TTTGTAGCTAA‑TGA‑TTTTAGCTAACTCAGCTG‑TTGAAATGAGCTGTGA‑TTGAGATGTATCC‑GGGAG‑TTTGAATGC‑GCTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAGAAAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGGAAAACG‑ttt                                                                                                                                                                                                                                                                                          <  1:375996/236‑1 (MQ=255)                 ggTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGAATGG‑TTTGAGA‑TTTGTAGCTAATTGA‑TTTTAGCTAACTCAGCTG‑TTGAAATGAGCTGTGA‑TTGAGATGTATCC‑GGGAG‑TTTGAATGCAGCTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGGAAAACG‑TTTC‑GGGCtcg                                                                                                                                                                                                                                                                                 <  1:376000/236‑1 (MQ=255)                                 aattGTCCTGACAAAGCCATTTACGAATGGTTTTGAGA‑TTTGTAGCTAA‑TGA‑TTTTAGCTAACTCAGCTG‑TTGAAATGAGCTGTGA‑TTGAGATGTATCC‑GGGAG‑TTTGAATGC‑GCTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACGTTTTC‑GGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTg                                                                                                                                                                                                                                                      >  1:376002/3‑244 (MQ=255)                                               aGCCATTTACGAATGG‑TTTGAGATTTTGTAGCTAATTGATTTTTAGCTAACTCAGCTGTTTGAAATGAGCTGTGATTTGAGATGTATCC‑GGGAGTTTTGAATGC‑GCTCAT‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACGTTTTC‑GGGCt                                                                                                                                                                                                                                                                                   >  1:1263870/1‑209 (MQ=255)                                                       aCGAATGGTTTTGAGA‑TTTGTAGCTAA‑TGA‑TTTTAGCTAACTCAGCTG‑TTGAAATGAGCTGTGA‑TT‑AGATGTATCC‑GGGAG‑TTTGAATGC‑GCTCA‑‑‑‑TTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACG‑TTTC‑gg                                                                                                                                                                                                                                                                                      >  1:973018/1‑188 (MQ=255)                                                       aCGAATGG‑TTTGAGA‑TTTGTAGCTAA‑TGA‑TTTTAGCTAACTCAGCTG‑TTGAAATGAGCTGTGA‑TTGAGATGTATCC‑GGGAG‑TTTGAATGC‑GCTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACG‑TTTC‑gg                                                                                                                                                                                                                                                                                      >  1:1159714/1‑190 (MQ=255)                                                                         ttGTAGCTAA‑TGA‑TTTTAGCTAACTCAGCTG‑TTGAAATGAGCTGTGA‑TTGAGATGTATCCGGGGAGTTTTGAATGC‑GCTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGCTTTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACGTTTTCGGGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGc                                                                                                                                                                                                                            >  1:376003/1‑234 (MQ=255)                                                                           gTAGCTAA‑TGA‑TTTTAGCTAACTCAGCTG‑TTGAAATGAGCTGTGA‑TTGAGATGTATCCGGGGAG‑TTTGAATGC‑GCTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACGTTTTC‑GGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGTG‑ATGCGATCTGGATGCCTg                                                                                                                                                                                       >  1:376004/1‑265 (MQ=255)                                                                                          ttAGCTAACTCAGCTG‑TTGAAATGAGCTGTGA‑TTGAGATGTATCC‑GGGAG‑TTTGAATGC‑GCTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACGTTTTCGGGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGTGTATGCGATCTGGATGCCTGA‑TTTTTACATGACATCATGACGCG‑CGAGAAA‑Gtt                                                                                                                                                  >  1:376007/1‑287 (MQ=255)                                                                                          ttAGCTAACTCAGCTG‑TTGAAATGAGCTGTGA‑TTGAGATGTATCC‑GGGAG‑TTTGAATGC‑GCTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACG‑TTTC‑GGGCTCGGGGTC‑GGGGTCACTACCGATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGTG‑ATGCGATCTGGATGCCTGA‑TTTTTACATGACATCA‑GACGCG‑CGAGaa                                                                                                                                                       >  1:1248032/1‑280 (MQ=255)                                                                                                       cTG‑TTGAAATGAGCTGTGA‑TTGAGATGTATCC‑GGGAG‑TTTGAATGC‑GCTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGGAAAACG‑TTTC‑GGGCtcg                                                                                                                                                                                                                                                                                 <  1:376005/152‑1 (MQ=255)                                                                                                                             tGAGATGTATCC‑GGGAGTTTTGAATGC‑GCTCATTTTTTGCCACCTCAGTGATTGAGATATTTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACGTTTTC‑GGGCTCGGGGTCGGGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGTG‑ATGCGATc                                                                                                                                                                                                 >  1:1080145/1‑213 (MQ=255)                                                                                                                                            gAG‑TTTGAATGC‑GCTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGCTTTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACGTTTTCGGGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGTG‑ATGCGATCTGGATGCCTGA‑‑TTTTACATGACATCA‑G‑CGCG‑CGAGAAA‑GTT‑AGTAGCATTTTGCATTC‑TTTT‑GTTAAGATGTAAAATTTTCA‑G‑TTT‑GCGCATGCG‑ACAGAC‑TTGCGAAGAGc                                                                   >  1:376010/1‑308 (MQ=255)                                                                                                                                                          gcTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACGTTTTC‑GGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGTG‑ATGCGATCTGGATGCCTGA‑‑TTTTACATGACAT‑A‑GACGCG‑CGAGAAA‑GTTGAGTAGCATTTTGCATTCTTTTG‑TTTAAGATGTaaa                                                                                                             >  1:376011/1‑259 (MQ=255)                                                                                                                                                                          cTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACG‑TTTC‑GGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGTG‑ATGCGATCTGGATGCCTGA‑‑TTTTACATGACATCA‑GACGCGACGAGAAATGTT‑AGTAGCATTTTGCATTC‑ttttgttttaagat                                                                                                                 >  1:376013/1‑231 (MQ=255)                                                                                                                                                                           tCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACG‑TTTCGGGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGA‑TTAGCCGTACTGTG‑ATGCGATCTGGATGCCTGA‑‑TTTTACATGACATCA‑GACGCG‑CGAGAAA‑GTT‑AGTAGCATTTTGCATTC‑TTTG‑‑TTAAGATGTAAAATTTTCA‑G‑TTTGGCGCATGCG‑ACAGAC‑TTGCGAAGAGCTGAGTATGTTCC‑TTGAGATACTCGACAACCTCTTca                              >  1:376014/1‑314 (MQ=255)                                                                                                                                                                                         a‑tTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGGAAAACG‑ttt                                                                                                                                                                                                                                                                                          <  1:1122542/69‑1 (MQ=255)                                                                                                                                                                                             ggCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACG‑TTTC‑GGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGCG‑ATGCGATCTGGATGCCTGA‑‑TTTTACATGACATCA‑GACGCG‑CGAGAAA‑GTT‑AGTAGCATTTTGCATTC‑TTTG‑TTTAAGATGTaa                                                                                                              >  1:376016/1‑224 (MQ=255)                                                                                                                                                                                                                     attGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACGTTTTCGGGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGTG‑ATGCGATCTGGATGCCTGA‑‑TTTTACATGACATCA‑GACGCG‑CGAGAAA‑GTT‑AGTAGCATTTTGCATTC‑TTTG‑TTTAAGATGTAAAATTTTCA‑GTTTTGGCGCATGCG‑ACAGAC‑TTGCGAAGAGCTGAGTATGTTCC‑TTGAGATACTCGACAACCTCTTCCATg                           >  1:376019/1‑283 (MQ=255)                                                                                                                                                                                                                     attGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACGTTTTC‑GGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGTG‑ATGCGATCTGGATGCCTGA‑‑TTTTACATGACATCA‑GAcgc                                                                                                                                                               >  1:376018/1‑159 (MQ=255)                                                                                                                                                                                                                      ttGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACGTTTTCGGGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGTG‑ATGCGATCTGGATGCCTGA‑TTTTTACATGACATCA‑GACGCG‑CGAGAAA‑GTT‑AGTAGCATTTTGCATTC‑TTTG‑TTTAAGATGTAAAATTTTCA‑G‑TTTGGCGCATGCG‑ACAGAC‑TTGCGAagag                                                                    >  1:376020/1‑242 (MQ=255)                                                                                                                                                                                                                                       gtaATGAAGGCAGAAGG‑AAACGTTTTC‑GGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGTG‑ATGCGATCTGGATGCCTGA‑‑TTTTACATGACATCA‑GACGCG‑CGAGAAA‑GTT‑AGTAGCATTTTGCATTC‑TTTG‑TTTAAGATGTaa                                                                                                              >  1:376022/1‑185 (MQ=255)                                                                                                                                                                                                                                             gaGGCAGAAGG‑AAACG‑TTTC‑GGGCTCGGGGTCGGGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCACTTTTTAGCTGATTTAGCCGTACTGTG‑ATGCGATCTGGATGCCTGATTTTTTACATGACATCA‑GACGCG‑CGAGAAA‑GTT‑AGTAGCATTTTGCATTC‑TTTG‑TTTAAGATGTAAAATTTTCATGTTTTGGCGCATGCGAACAGACTTTGCGAAGAGCTGAGTATGTTCCTTTGAGATACTCGACAACCTCTTCCATGGACGCAGGATCGTTAAAGGATTGAg  >  1:1142281/2‑290 (MQ=255)                                                                                                                                                                                                                                             aaGGCAGAAGG‑AAACGTTTTC‑GGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCACTTTTTAGCTGA‑TTAGCCGTACTGTG‑ATGCGATCTGGATGCCTGA‑TTTTTACATGACATCA‑GACGCG‑CGAGAAA‑GTT‑AGTAGCATTTTGCATTC‑TTTGTTTTAAGATGTAAAATTTTCA‑G‑TTTGGCGCATGCG‑ACAGAC‑TTGCGAAGAGCTGAGTATGTTCCTTTGAGAt                                               >  1:376023/1‑240 (MQ=255)                                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                                                            GATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGAATGG‑TTTGAGA‑TTTGTAGCTAA‑TGA‑TTTTAGCTAACTCAGCTG‑TTGAAATGAGCTGTGA‑TTGAGATGTATCC‑GGGAG‑TTTGAATGC‑GCTCA‑‑TTTTGCCACCTCAGTGATTGAGATA‑TTGGCAAAG‑AAAGC‑TTTAAGCATTATTGAATTAGTAGGGGTAGTAATGAAGGCAGAAGG‑AAACG‑TTTC‑GGGCTCGGGGTC‑GGGGTCACTACC‑ATCACCTGAATCTGATGATAAGGCAC‑TTTTAGCTGATTTAGCCGTACTGTG‑ATGCGATCTGGATGCCTGA‑TTTTTACATGACATCA‑GACGCG‑CGAGAAA‑GTT‑AGTAGCATTTTGCATTC‑TTTG‑TTTAAGATGTAAAATTTTCA‑G‑TTTGGCGCATGCG‑ACAGAC‑TTGCGAAGAGCTGAGTATGTTCCTTTGAGATACTCGACAACCTCTTCCATGGACGCAGGATCGTTAAAGGATTGAG  >  NC_000913/294993‑295497

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑