Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	581,227	A→C	22.4%	I132L (ATC→CTC)	nohD →	DLP12 prophage; DNA packaging protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	581,227	0	A	C	22.4%	51.0 / 14.0	27	I132L (ATC→CTC)	nohD	DLP12 prophage; DNA packaging protein
Reads supporting (aligned to +/- strand):  ref base A (8/13);  new base C (3/3);  total (11/16)
Fisher's exact test for biased strand distribution p-value = 6.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.19e-01

ACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCG  >  NC_000913/581088‑581365                                                                                                                                            |                                                                                                                                           aCGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGa                                                                                                                                            >  2:705205/1‑140 (MQ=32) aCGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGa                                                                                                                                            >  1:908797/1‑140 (MQ=32)          aCTTACGCGTGCGCAGGCCGATGCACCGGAGCTGAAAAATGCCAGAGCCTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGTATCCCCCTGt                                                                                                                                   <  1:1334896/140‑1 (MQ=12)            ttACGCGTGCGCAGGCCGTTGCACAGGAGCTGAAAATTGCCAGAGACTCCGCTGATGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCg                                                                                                                                 <  2:698179/140‑1 (MQ=12)            ttACGCGTGCGCAGGCCGATGCACAGGAGCTGAATAATGCCAGAGACTCCGCTGTAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGTTGAAAGTGCCAGTATTCTCGACGGGATCCCCCTGTCg                                                                                                                                 <  2:109853/140‑1 (MQ=255)            ttACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCg                                                                                                                                 <  2:540493/140‑1 (MQ=32)            ttACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCg                                                                                                                                 <  2:1362209/140‑1 (MQ=32)            ttACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCg                                                                                                                                 <  2:698336/140‑1 (MQ=32)            ttACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCg                                                                                                                                 <  2:932569/140‑1 (MQ=32)            ttACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCg                                                                                                                                 <  2:1014172/140‑1 (MQ=32)            ttACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTCGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCg                                                                                                                                 <  2:21280/140‑1 (MQ=17)             tACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCgg                                                                                                                                <  1:1540726/140‑1 (MQ=32)             tACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCgg                                                                                                                                >  2:1642390/1‑140 (MQ=32)              aCGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGt                                                                                                                               >  1:1462941/1‑140 (MQ=32)                   tGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAgc                                                                                                                          >  1:64758/1‑140 (MQ=32)                   tGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAgc                                                                                                                          >  1:1285861/1‑140 (MQ=32)                    gcgcAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAgcg                                                                                                                         >  1:693748/1‑140 (MQ=32)                     cgcAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAgcgg                                                                                                                        >  1:1264540/1‑140 (MQ=32)                       cAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAgcggcg                                                                                                                      <  2:744179/140‑1 (MQ=32)                              aTGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTTCCg                                                                                                               >  2:98701/1‑140 (MQ=31)                                      gaacTGAAGAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGTTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGCTCCCCCTGTCg                                                                                                                                 <  2:1676760/111‑1 (MQ=1)                                      gaacTGAAGAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGTTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGCTCCCCCTGTCg                                                                                                                                 <  2:1676755/111‑1 (MQ=1)                                      gaacTGAAGAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGTTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGCTCCCCCTGTCg                                                                                                                                 <  2:1075252/111‑1 (MQ=1)                                      gaacTGAAGAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGTTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGCTCCCCCTGTCg                                                                                                                                 >  1:1676760/4‑114 (MQ=1)                                      gaacTGAAGAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGTTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGCTCCCCCTGTCg                                                                                                                                 >  1:1676755/4‑114 (MQ=1)                                      gaacTGAAGAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGTTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGCTCCCCCTGTCg                                                                                                                                 >  1:1075252/4‑114 (MQ=1)                                                                                 cagtCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTACCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGcc                                                            <  2:29891/137‑1 (MQ=1)                                                                                                              gccggTGAAAGTGCCAGTAGTCTCGCCGGGAGCCCCCGGTCGGTGCAGCGGCGTTTTCCGGACCTGGAACCCCGACATGTGGATTGCCTGACACGGGCTATCCTCAAAGCCATGAACCACGCAGCCGCGCTGGATGAACt                               <  2:1330224/137‑1 (MQ=1)                                                                                                                                           gATCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCg  >  2:492183/1‑140 (MQ=32)                                                                                                                                            |                                                                                                                                           ACGCCATCGACTTACGCGTGCGCAGGCCGATGCACAGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCG  >  NC_000913/581088‑581365

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑