Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	581,289	0	A	G	70.4%	22.5 / 12.1	27	K152K (AAA→AAG)	nohD	putative DNA‑packaging protein NohD
Reads supporting (aligned to +/- strand):  ref base A (5/3);  new base G (10/9);  total (15/12)
Fisher's exact test for biased strand distribution p-value = 6.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GCTGCAGGCCAGCGAGACAGATCTCCAGCCAGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGA‑TCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAA‑ACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCCGCATACCAGGAAGGGCGCTGGGAAACACTGCCC  >  NC_000913/581040‑581518                                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                      gctgcAGGCCAGCGAGACAGATCTCCAGCCAGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGA‑TCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCATGAA‑Ac                                                                                                                                                                                                                                      >  1:122829/1‑251 (MQ=17)                    gATCTCCAGCCAGGGATTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGAGAAACTGCCAGTATTCTCGACGGGA‑TCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAACCCGACATGTTGATTTCCTGAA‑ACGGGATATCATCAAAGCCAt                                                                                                                                                                                                                   >  1:175336/1‑251 (MQ=9)                                             aCGAACGCCATTGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGA‑TCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAA‑ACGGGATATCATCAAAg                                                                                                                                                                                                                       <  1:3542/222‑1 (MQ=14)                                                                                    aggaactaaaaaaTGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGAGGATGGCCGGAGACGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTc                                                                                                                                                    >  1:77666/9‑250 (MQ=255)                                                                                               aatgcaaaagattCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTTATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACAGCATTAAAGCCATGAACAAATCAGCTGCGCTGGATGAAATAATACCGTGGTTGCTGAGTGAATATATCGAACAGTCAGGTTaaggggc                                                                                                                                        <  1:120193/239‑6 (MQ=255)                                                                                                     aaagattCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGcagc                                                                                                                                  <  1:41001/245‑4 (MQ=2)                                                                                                         attCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTaaggggcttcagcacnc                                                                                                                              <  1:136550/249‑16 (MQ=2)                                                                                                             cGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcg                                                                                                                          <  1:72937/251‑8 (MQ=2)                                                                                                                 naaGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGA‑TCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGACACCCGACATGTTGATTTCCTGAA‑ACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGaaa                                                                                                                                                        >  1:22387/2‑216 (MQ=17)                                                                                                                    ggggtggAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcgcgcgcgg                                                                                                                   >  1:159252/3‑237 (MQ=255)                                                                                                                     tggtggAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcgcgcgcggg                                                                                                                  >  1:13835/1‑236 (MQ=255)                                                                                                                       gtggAAACCGCATTCTGCACGTTCGTGCTGTCGCTGATGGCCGGAGAAGAAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGCCATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcgcgcgcgggtc                                                                                                                >  1:39174/1‑234 (MQ=2)                                                                                                                         ggAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCAGAGAAGTAGCCAACATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGAGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCCGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcgcgcgcgggtct                                                                                                               >  1:98379/1‑232 (MQ=255)                                                                                                                              ccGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcgcgcgcgggtctactttc                                                                                                         <  1:50260/251‑25 (MQ=255)                                                                                                                              ccGCAGTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATAGTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTGGCGGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCGGCactctgcgctctcgggtcttctttc                                                                                                         <  1:135619/251‑25 (MQ=255)                                                                                                                               cGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTG‑CTGGAGTTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAACACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAACTAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcac                                                                                                                                >  1:94972/1‑226 (MQ=2)                                                                                                                                  aTTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATCTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCGGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcgcgcgcggg                                                                                                                  <  1:121768/238‑16 (MQ=255)                                                                                                                                                                              gTATTCTCGACGGGA‑TCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAA‑ACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAgg                                                                                               <  1:50281/213‑1 (MQ=255)                                                                                                                                                                                                                  cgcttcccGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCGCGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGa                        >  1:138083/7‑249 (MQ=255)                                                                                                                                                                                                                    nttcccGGAGCTGGAAAACCGACATATTGATTTCCTCAAGACGG‑ACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGGTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGcag                                                                                                                                   >  1:103802/5‑138 (MQ=255)                                                                                                                                                                                                                    nnncccNGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGcac                                                                                                                                   <  2:103802/136‑3 (MQ=9)                                                                                                                                                                                                                         cGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACAGCATGAAAGCCATGAACAAAGCAGCTGCGCGGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCGCGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGTCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTg               <  1:88546/251‑1 (MQ=255)                                                                                                                                                                                                                              ntGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCCGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCGCGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGagtcg                                   >  1:37707/2‑222 (MQ=9)                                                                                                                                                                                                                                ggAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGCCCAAAGCAGCTGAGCTGGATGAAATCATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCGCGCGCGGGTATACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCCGACGATAATTACTATTTACCCAAAGAGTCGGCCTACCAGGACGGGCGCTGGGAAacg        >  1:128682/1‑250 (MQ=255)                                                                                                                                                                                                                                      ccGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCGCGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTGGGAAacgttgccg  >  1:5438/1‑244 (MQ=255)                                                                                                                                                                                                                                              ttGATTTCCTGAA‑ACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCcgcgn                                                                                                                     <  1:109241/128‑2 (MQ=255)                                                                                                                                                                                                                                              ttGATTTCCTGAA‑ACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCgcgc                                                                                                                     >  2:109241/1‑128 (MQ=255)                                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                      GCTGCAGGCCAGCGAGACAGATCTCCAGCCAGGGACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGA‑TCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAA‑ACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCCGCATACCAGGAAGGGCGCTGGGAAACACTGCCC  >  NC_000913/581040‑581518

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑