Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	281,089	0	A	C	71.4%	‑1.5 / 12.3	21	Y299D (TAT→GAT)	yagA	CP4‑6 prophage; putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (1/5);  new base C (0/15);  total (1/20)
Fisher's exact test for biased strand distribution p-value = 2.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.60e-03

ACCCGTTCTCCCCTGAACGCCTTGCCTGCGCTCAGACTTACCCCTTTCACGCTCAGCTTTCCGCTGATATCCACTTTCCTGACCATCACCCCTTCATCGTATTCCGGGGGCG‑TTGTGTTGCCGCTGTACTGCCGCGCTGACGGCTGATACCGCGAGCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGACCGTCCGCCAGTGGTCGAAGGCGCGCTGCAGTTCACCGCTGTCTGCGAACCATTTTCCCTGCAGCACTT  >  NC_000913/280941‑281214                                                                                                                                                      |                                                                                                                              aCCCGTTCTCCCCTGAACGCCTTGCCTGCGCTCAGACTTACCCCTTTCACGCTCAGCTTTCCGCTGATATCCACTTTCCTGACCATCACCCCTTCATCGTATTCCGGGGGCG‑TTGTGTTGCCGCTGTACTGCCGCGCTGACGGCTGATAc                                                                                                                              <  2:175699/150‑1 (MQ=255)              tGAACGCCTTGCCTGCGCTCAGACTTACCCCTTTCACGCTCAGCTTTCCGCTGATATCCACTTTCCTGACCATCACCCCTTCATCGTATTCCGGGGGCG‑TTGTGTTGCCGCTGTACTGCCGCGCTGACGGCTGATACCGCGAGCCCGGTAc                                                                                                                <  1:276932/151‑1 (MQ=255)                             cccTCAGCCTTCCCCCTTCCCCGCTCAGCTTCCCGCTGATATCCCCTTCCCTGACCACCCCCCCTTCATCGTATTCCGGGGGCG‑TTGTGTTGCCGCTGTACTGCCGCGCTGACGGCTGATACCGCGAGCCGGGTACCGCCATATCCAgcgc                                                                                                 <  2:129894/149‑1 (MQ=255)                                         ccccTTTCCCCCTCAGCTTCCCGCTGATCCCCCTTTCCCTGCCCACCCCCCCTTCATCGTATCCCGGGGGCG‑TTGTTTTCCCGCTGTCCTGCCGGGCTGACGGCTGATACCGCGGCCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGCg                                                                                     <  2:98934/151‑1 (MQ=255)                                                        tcTTTCCGTTGATCCCCCCTTCCCCGCCCCCCCCCCCTCCCTCGTATTCCGGGGGCG‑TTGTTTTCCCGTTGTCCTCCCGCGCTGCCGGCTAATCCCGCGAGCCCGTTCCCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGAc                                                                      <  2:45506/150‑1 (MQ=255)                                                        ctttcccGCTGATTCCCCCTTCCCGGACCATCCCCCCTTCATCGTATCCCGGGGGCT‑TTGTTTTGCCGCTGTACTGCCGCGGTGACGGCTGATCCCGCGGGCCGGGTTCCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGAc                                                                      <  2:196588/146‑1 (MQ=255)                                                        ccTTTCCGCTGATTCCCCCTTCCCTGACCATCCCCCCTTCATCGTATTCCGGGGGGG‑TTTTTTTGCCGCTGTACGGCCGCGCTGAGGGTTGATCCCGCGAGCCCGTTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGAc                                                                      <  2:66736/150‑1 (MQ=255)                                                        ccTTTCCGCTGATCTCCACTTTCCTGCCCCTCCCCCCTTCATCGTGTTCCGGGGGCG‑TTGTGTTGCCGCTGTACTGCCGCGCTGGCGGCTGATACCGCGAGCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGAc                                                                      <  2:250542/150‑1 (MQ=255)                                                         cTTTCCGCTTATCCCCCCTTTCCTGCCCATCCCCCCTTCATCGTTTCCCGGGGGCG‑TTGTGTTGCCGCGTTCGTGCCGCGCTGGGGGCTGATCCCGCGAGCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGAc                                                                      <  2:126825/150‑1 (MQ=255)                                                         cTTTCCGCTGATACCCCCTTTCCGGACCACCCCCCCTTCATCGTATTCGGGGGGCG‑TTGTGTTGCCGCTGTACTGCCGCGCTGACGGCTGATCCCGCGAGCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAg                                                                        <  2:270445/148‑1 (MQ=255)                                                         cTTCCCGCTTATTTCCCCTTTCCCGCCCATCCCCCCTCCACCGTATCCGGGGGGCG‑TTGTGTTGCCGCTGTCCCGCCGCGCTGACGGCTGATCCCGCGAGCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGAc                                                                      <  2:9714/150‑1 (MQ=255)                                                                                      cccccccTCCATCGTATCCGGGGGGCG‑TTGTGTGCCCGCTGTACGGCCGCGCGGACGGCTGAACCCGCGGGCCGGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGACCGTCCGCCAGTGGTCGAAGGCGCGCTGCAg                                        <  2:129649/148‑1 (MQ=255)                                                                                         ccccTTCATCGTATCCGGGGGGGT‑TTGTGTTGCCGCTGTCCGGCCGCGGGGCCGGCTAATCCCGCGGGCCGGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGACCGTCCGCCAGTGGTCGAAGGCGCGCTGCAGTTc                                     <  2:197071/151‑1 (MQ=255)                                                                                         ccccTTCATCGTATCCGGGGGGCG‑TGGTGTTCCCGCTGTCCTGCCGCGCGGCCGGCTGATCCCGCGAGCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGACCGTCCGCCAGTGGTCGAAGGCGCGCTGCAGTTc                                     <  2:405064/151‑1 (MQ=255)                                                                                              tcccctcttccggggggCT‑TTGTTTGCCCGCTGTCCTCCCGGGCTGCCGGTTGATCCCGGGGCCCCGTTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGACCGTCCGCCAGTGGTCGAAGGCGCGCTGCAGTTCACCGc                                <  2:182309/139‑1 (MQ=255)                                                                                              tcaccgtttccgggggggG‑TTGTGTCGCCCCTTTCCCCCCGCGCTGCGGGCTGATCCCGCGGCCCGGGGCCCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGACCGTCCGCCAGTGGTCGAAGGCGCGCTGCAGTTCACCGc                                <  2:73934/139‑1 (MQ=255)                                                                                               cccgcgtttCCGGGGGGGTTTGTGTTCCCCCTTCCCGCCCGCGCGGGCGGCTGACCCCGCGGCCCCGGTCCCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGACCGTCCGCCAGTGGTCGAAGGCGCGCTGCAGTTCACCGc                                <  2:74386/144‑1 (MQ=255)                                                                                                                  ttGTGTTGCCCCTGTCCGGCCGCGCGGACGGCTGATCCCGCGAGCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGACCGTCCGCCAGTGGTCGAAGGCGCGCTGCAGTTCACCGCTGTCTGCGAACCATTTTc              <  2:271316/150‑1 (MQ=255)                                                                                                                  ttGTGTGGCCGCGGTCCGCCCGCGCGGACGGCTAAACCCGCGAGCCGGGTCCCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGACCGTCCGCCAGTGGTCGAAGGCGCGCTGCAGTTCACCGCTGTCTGCGAACCATTTTcc             <  2:401469/151‑1 (MQ=255)                                                                                                                  ttGTGGCGCCGCTGTACGGCCGCGCTGACGGCTGATCCCGCGCGCCGGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGACCGTCCGCCAGTGGTCGAAGGCGCGCTGCAGTTCACCGCTGTCTGCGAACCATTTTcc             <  1:337338/151‑1 (MQ=255)                                                                                                                             cTGTACTGCCGCGCTGACGGCTGATACCGCGAGCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGACCGTCCGCCAGTGGTCGAAGGCGCGCTGCAGTTCACCGCTGTCTGCGAACCATTTTCCCTGCAGCACtt  >  1:183985/1‑151 (MQ=255)                                                                                                                                                      |                                                                                                                              ACCCGTTCTCCCCTGAACGCCTTGCCTGCGCTCAGACTTACCCCTTTCACGCTCAGCTTTCCGCTGATATCCACTTTCCTGACCATCACCCCTTCATCGTATTCCGGGGGCG‑TTGTGTTGCCGCTGTACTGCCGCGCTGACGGCTGATACCGCGAGCCCGGTACCGCCATATCCAGCGCCTCGTGCGGGCGTTCAAGGTTATAGACCGTCCGCCAGTGGTCGAAGGCGCGCTGCAGTTCACCGCTGTCTGCGAACCATTTTCCCTGCAGCACTT  >  NC_000913/280941‑281214

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑