Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	283,931	0	T	G	60.9%	7.5 / 17.2	25	V244G (GTG→GGG)	yagF	CP4‑6 prophage; dehydratase family protein
Reads supporting (aligned to +/- strand):  ref base T (2/7);  new base G (10/4);  total (14/11)
Fisher's exact test for biased strand distribution p-value = 3.61e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.21e-02

CGGGCAAGGTGCAGACCATCGGCGCGCGTTTCGCCAACCACGAACTCTCCCTGCAGGAGGCCGCCGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCAGGTGGTCGCGGAGGCGCTGGGTCTGGCGCTGCCGCACTCCGCGCTGGCGCCGTCCGGGCAGGCGGTGTGGCTGGAGATCGCCCGCCAGTCGGCGCGCGCGGTCAGCGAGCTGGATAGCCGCGGCATCACCACGCGGGATATCCTCTCCGATA  >  NC_000913/283793‑284080                                                                                                                                           |                                                                                                                                                      cgGGCAAGGTGCAGACCATCGGCGCGCGTTTCGCCAACCACGAACTCTCCCTGCAGGAGGCCGCCGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGGGTCAGTTCCTCGGCACGGCGGGGACCTCGCCGGGGGGCGCGggggg                                                                                                                                           >  2:526193/1‑150 (MQ=255)        ggTGCAGACCATCGGCGCGCGTTTCGCCAACCACGAACTCTCCCTGCAGGAGGCCGCCGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCCGGGGGTCGCGGAGGCGCTgggg                                                                                                                                    >  2:520130/1‑150 (MQ=255)         gTGCAGACCATCGGCGCGCGTTTCGCCAACCACGAACTCTCCCTGCAGGAGGCCGCCGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCAGGGGGTCGCGGGGGCGCTGGGt                                                                                                                                    >  2:348016/1‑150 (MQ=255)                       cgcgcgTTTCGCCAACCACGAACTCTCCCTGCAGGAGGCCGCCGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCAGGTGGTCGCGGAGGCGCTGGGTCTGGCGCTGCCGCAc                                                                                                                     <  2:301599/151‑1 (MQ=255)                               tCGCCAACCACGACCTCTCCCGGCAGGAGGCCGCCGACCTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCAGGTGGTCGCGGAGGCGCTGGGTCTGGCGCTGCCGCACTCcgcgac                                                                                                             <  1:163296/151‑3 (MQ=255)                                     aCCACGAACTCTCCCTGCAGGAGGCCGCCGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTATCAGTTCCTCGGCACGGCGGGCACCTCGCAGGCGGGCGCGGAGGCGCTGGGTCTGGCCCTGGCCCACTCCCCGCTGgcgc                                                                                                        >  1:526610/1‑150 (MQ=255)                                           aaCTCTCCCTGCAGGAGGCCGCCGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCAGGGGGTCGCGGAGGCGCTGGGTCTGGCGCTGCCGCACTCCGCGCCGGCGcccgcccg                                                                                                 >  1:634632/1‑145 (MQ=255)                                             ctctCCCTGCAGGAGGCCGCCGAACTGGGCTGTGGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCCGGGGGTCGCGGAGGCGCTGGGTCTGGCGCTGCCGCACTCCGCGCTGGCGCCGTCCgggg                                                                                               >  1:150688/1‑150 (MQ=255)                                             ctctCCCTGCAGGAGGCCGCCGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCAGGGGGTCGCGGAGGCGCTGGGTCTGGCGCCGCCGCACTCCCCCCTGGCGCCGGCCggg                                                                                                >  1:543127/1‑150 (MQ=255)                                             ctctCCCTGCAGGAGGCCGCCGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCCCGCAGGGGGGCGCGGAGGGGCTGGGGCTGGCGCCGCCGCACTCCGCGCTGGCGCCGTCCggg                                                                                                >  2:181524/1‑150 (MQ=255)                                                 cccTGCAGGCGGCCGCCGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCCCCTCCCAGGGGGTCGCGGAGGCGCTGGGTCTGGCGCCGCCGCACTCCGCGCTGGCGCCGTCccggccggg                                                                                           >  1:57037/1‑150 (MQ=255)                                                   cTGCAGGAGGCCGCCGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCCCCTCGCAGGGGGTCCCGGGGGGGCCGGGGCTGGGGCTGCCCCCCCCCGCGCTGGCGCCGCCCggggcggggg                                                                                         >  2:14863/1‑144 (MQ=255)                                                   cTGCAGGAGGCCGCCGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCAGGGGGGCGCGGAGGCGCTGGGTCTGGCGCTGCCGCACTCCCCGCTGGCGCCGTCCGGGCAGGCgg                                                                                         >  1:306687/1‑151 (MQ=255)                                                         gaggCCGCCGAACTGGGCTGGCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCAGGTGGTCGCGGAGGCGCTGGGTCTGGCGCTGCCGCACTCCGCGCTGGCGCCGTCCGGGCAGGCGGTGTgg                                                                                    <  2:552572/150‑1 (MQ=255)                                                            gccgccGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCAGGTGGTCGCGGAGGCGCTGGGTCTGGCGCTGCCGCACTCCGCGCTGGCGCCGTCCGGGCAGGCGGTGTGGCTg                                                                                 <  1:310140/150‑1 (MQ=255)                                                                ccgAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCAGGTGGTCGCGGAGGCGCTGGGTCTGGCGCTGCCGCACTCCGCGCTGGCGCCGTCCGGGCAGGCGGTGTGGCTGgaga                                                                             <  1:610907/150‑1 (MQ=255)                                                                  gAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGCGTCAGTTCCTCGGCACGGCGGGCCCCTCGCCGGCGGCCGCCGAGGCGCTGGGGCCGGCGCTGCCGCACTCCGCCCTGGCGCCGTCCGGGCAGGCGGCGTGGGTGGGGAttg                                                                          >  2:447875/1‑149 (MQ=255)                                                                          cTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCAGGTGGGCGCGGAGGCGCTGGGTCTGGCGCTGCCGCACTCCGCGCTGGCGCCGTCCGGGCAGGCGGGGTGGCTGGAGATCGCCCGCCAg                                                                  >  1:180894/1‑151 (MQ=255)                                                                                                         tgtgggTTCCTGGGCACGGCGGGCCCCTCGCAGGTGGTCGCGGAGGCGCTGGGTGTGGCGCTGCCGCACTCCGCGCTGGCGCCGCCCGGGCAGGCGGTGTGGCGGGAGATCGCCCGCCAGTCGGCGCGCGCGGTCAGCGAGCTGGATAGc                                    <  2:369259/145‑1 (MQ=255)                                                                                                          gacggTTCCGCGGTCCGGCGGGCCCCTCGCGGGGGGTCGGGGAGGCGCTGGGCGTGGCCCGGCGCCATTCCGCGCGGTCGCGGACCGGGCGGGGGGTGTGGCTGGAATTCGCCCGCCAGTCGGCGCGCGCGGTCAGCGAGCTGGATAGcc                                   <  2:439584/146‑1 (MQ=255)                                                                                                                                 cccccGCAGGGGGGGGGGGGGGGGCGGGGTCGGGCGCTGCCGCACTCCGCGCTGGCGCCGTCCGGGCAGGCGGTGTGGCGGGAGATCGCCCGCCAGTCGGCGCGCGCGGTCAGCGAGCTGGATAGCCGCGGCATCACCACGCGGGATATcc           <  2:383574/147‑1 (MQ=255)                                                                                                                                 cccTCGAAGGGGGGCGCGGGGGCGTGGGTTTTGGTGGGGCGGCTCTCCGGGGTGGCGCCGCCCGGGCAGGGGGGGTTGCGGGAGAGCCCCCGCCAGTCGGCGCGCGCGGTCAGCGAGCTGGATAGCCGCGGCATCACCACGCGGGATATcc           <  1:388098/150‑1 (MQ=255)                                                                                                                                  ccgcgcgGGGGGTCGGGGGGGCGCTGGGTCTGGCGCGGCCGCACCCCGCGCTGGCGCCGTCCGGGCGGGGGGTGTGGCTGGAGATCGCCCGCCAGTCGGCGCGCGCGGTCAGCGAGCTGGATAGCCGCGGCATCACCACGCGGGATATCct          <  2:38929/148‑1 (MQ=255)                                                                                                                                  ccTCGCAGGTGGTCGCGGAGGCGCTGGGTCTGGCGCTGCCGCACTCCGCGCTGGCGCCGTCCGGGCAGGCGGTGTGGCTGGAGATCGCCCGCCAGTCGGCGCGCGCGGTCAGCGAGCTGGATAGCCGCGGCATCACCACGCGGGATATc            >  2:480921/1‑149 (MQ=255)                                                                                                                                   cTCGCGGGTGGTCGGGGGGGCGCTGGGTCTGGCGCTGCCGCCCCCCGCGCTGGCGCCGTCCGGGCAGGGGGTGTGGCGGGAGATCCCCCGCCAGTCGGCGCGCGCGGTCAGCGAGCTGGATAGCCGCGGCATCACCACGCGGGATATCctc         <  2:543423/151‑1 (MQ=255)                                                                                                                                         ggtggtCGCGGAGGCGCTGGGTCTGGCGCTGCCGCACTCCGCGCTGGCGCCGTCCGGGCAGGCGGTGTGGCTGGAGATCGCCCGCCAGTCGGCGCGCGCGGTCAGCGAGCTGGATAGCCGCGGCATCACCACGCGGGATATCCTCTCCGAt   >  1:319986/1‑151 (MQ=255)                                                                                                                                          gtggtCGCGGAGGCGCTGGGTCTGGCGCTGCCGCACTCCGCGCTGGCGCCGTCCGGGCAGGCGGTGTGGCTGGAGATCGCCCGCCAGTCGGCGCGCGCGGTCAGCGAGCTGGATAGCCGCGGCATCACCACGCGGGATATCCTCTCCGATa  >  1:587524/1‑151 (MQ=255)                                                                                                                                           |                                                                                                                                                      CGGGCAAGGTGCAGACCATCGGCGCGCGTTTCGCCAACCACGAACTCTCCCTGCAGGAGGCCGCCGAACTGGGCTGTCGCGCCTGCGCCTCGCCGGGCGGCGGGTGTCAGTTCCTCGGCACGGCGGGCACCTCGCAGGTGGTCGCGGAGGCGCTGGGTCTGGCGCTGCCGCACTCCGCGCTGGCGCCGTCCGGGCAGGCGGTGTGGCTGGAGATCGCCCGCCAGTCGGCGCGCGCGGTCAGCGAGCTGGATAGCCGCGGCATCACCACGCGGGATATCCTCTCCGATA  >  NC_000913/283793‑284080

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑