Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,405,758	G→A	intergenic (‑7/‑221)	mcaS ← / → smrA	small regulatory RNA McaS/DNA endonuclease SmrA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,405,758	0	G	A	96.4%	79.9 / NA	28	intergenic (‑7/‑221)	mcaS/smrA	small regulatory RNA McaS/DNA endonuclease SmrA
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (18/9);  minor base C (1/0);  total (19/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

GTGATGTTGCCGGTTAGCGAAATTTTACCGAAAGCGGCCTATTATTTGATTCAGCGGCGTGATAGTCGCCAGACACCACTGACCGCGTCATTAATCACGCAATTCCGGCGAGAATGCGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTGTTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACTTATTACTGGAAATTTGGGTAATACGTTGTTGGACCGACCCGGTCTGGTTATCATATCGCGCTCTTAATTGCGGGAGGATGTAACATGAACCTTGAC  >  NC_000913/1405515‑1405990                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                         gtgttGTTGCCGGTTAGCTAAACTGTCCCGAAAGCGGCCTATTAGTTGATTCAGCGTCGTGATAGTCGCCAGATCCCACTTCCCGCTTCATTAATCCCGCAATTCCGGCGCGAATGCGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACGCAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAAc                                                                                                                                                                                                                                   <  2:359495/247‑1 (MQ=255)          ccGGTTAGCGAAATTTTACCGAAAGCGGCCTATTATTTGATTCAGCGGCGTGATAGTCGCCAGACACCACTGACCGCGTCATTAATCACGCAATTCCGGCGAGAATGCGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAAc                                                                                                                                                                                                                          <  1:358555/251‑1 (MQ=255)                   gAAATTTTACCGAAAGCGGCCTATTATTTGATTCAGCGGCGTGATAGTCGCCAGACACCACTGACCGCGTCATTAATCACGCAATTCCGGCGAGAATGCGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTg                                                                                                                                                                                                                 <  1:416003/251‑1 (MQ=255)                    aaaTTTTACCGAAAGCGGCCTATTATTTGATTCAGCGGCGTGATAGTCGCCAGACACCACTGACCGCGTCATTAATCACGCAATTCCGGCGAGAATGCGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGc                                                                                                                                                                                                                >  1:334918/1‑251 (MQ=255)                    aaaTTTTACCGAAAGCGGCCTATTATTTGATTCAGCGGCGTGATAGTCGCCAGACACCACTGACCGCGTCATTAATCACGCAATTCCGGCGAGAATGCGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGc                                                                                                                                                                                                                <  1:397640/251‑1 (MQ=255)                      aTTTTACCGAAAGCGGCCTATTATTTGATTCAGCGGCGTGATAGTCGCCAGACACCACTGACCGCGTCATTAATCACGCAATTCCGGCGAGAATGCGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGcc                                                                                                                                                                                                               >  1:257476/1‑250 (MQ=255)                              gAAAGCGGCCTATTATGTGATTCAGCGGCGTTATAGTCGCCAGACACTACTGACCGCGTTATTAATCAAGCAATTCCGGCGAGAATGCGGCTATCTGCAAAGTTAAAACCGCATAAAAAAATAGAGTCTGTCGTCATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCTTCTTAAATCCGGCATTGTCTCCTCTGCGCCTGTGACTGTATTATAACGGTTTTACCCTTTAGTTGCCAATTttctt                                                                                                                                                                                                      <  2:365467/251‑1 (MQ=255)                                              ttGATTCAGCGGCGTGATAGTCGCCAGACACCACTGACCGCGTCATTAATCACGCAATTCCGGCGAGAATGCGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCa                                                                                                                                                                                       <  1:310270/250‑1 (MQ=255)                                                 aTTCAGCGGCGTGATAGTCGCCAGACACCACTGACCGCGTCATTAATCACGCAATTCCGGCGAGAATGCGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGCCTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGa                                                                                                                                                                                    >  2:446991/1‑250 (MQ=255)                                                             gATAGTCGCCAGACACCACTGACCGCGTCATTAATCACGCAATTCCGGCGAGAATGCGTCTATCTGCAAAGTTAAAACTGCAAAAAAAAATAGAGTCTTTCGACATCCGCCAGACTCTACAGTCCACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGGATTATAACGGTTTTAACCTTTAGTTGCCAATGTTCTGCAGTGACAGAGTTCACGAAAATATAAGTTAc                                                                                                                                                                       <  2:469997/251‑1 (MQ=255)                                                                   cGCCAGACACCACTGACCGCGTCATTAATCACGCAATTCCGGCGAGAATGCGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACattatt                                                                                                                                                                 >  1:195074/1‑251 (MQ=255)                                                                     ccAGACACCACTGACCGCGTCATTAATCACGCAATTCCGGCGAGAATGCGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACAttatta                                                                                                                                                                >  1:459749/1‑250 (MQ=255)                                                                          caccacTGACCGCGTCATTAATCACGCAATTCCGGCGCGAATGCGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTCTTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCg                                                                                                                                                          >  2:320919/1‑251 (MQ=255)                                                                                                                     cGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGc                                                                                                               <  1:4852/251‑1 (MQ=255)                                                                                                                                     tAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGAAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACttat                                                                                               >  1:314284/1‑251 (MQ=255)                                                                                                                                              aTAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACTTATTACTGGaa                                                                                       >  2:199576/1‑250 (MQ=255)                                                                                                                                                 aaaaaaTAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATACGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCTTAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACTTATTACTGGCAAttt                                                                                   >  1:500265/1‑251 (MQ=255)                                                                                                                                                  aaaaaTAGAATCTGACGCCATCCGCCAGACTCTACAGTACACCCAGCGATGCATCCGCGTCTTAAATCCGACATTGCCTCCTCTGCGCCGGTGACTGTAGTATAACGGGTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTAAATTATTAATATCGTGAATGCAAAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATTTTTGGACCTTATAACTGGAAATTTg                                                                                  >  2:330281/1‑251 (MQ=255)                                                                                                                                                    aaaTAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGACAATATAAGTTACATTATTAATATAGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCCATATTTGGAACTTATTACTGGAAATTTggg                                                                                >  1:214598/1‑251 (MQ=255)                                                                                                                                                      aTAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACTTATTACTGGAAATTTGGGt                                                                               >  1:392355/1‑250 (MQ=255)                                                                                                                                                        agagTCTGTCGACATCCGCCAGAATCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACTTATTACTGAAAATTTGGGTAAt                                                                            >  1:326087/1‑251 (MQ=255)                                                                                                                                                            tCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACTTATTACTGGAAATTTGGGTAATACgt                                                                        >  2:390547/1‑251 (MQ=255)                                                                                                                                                              tGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACTTATTACTGGAAATTTGGGTAATACgttg                                                                      >  1:464433/1‑251 (MQ=255)                                                                                                                                                                        cGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACTTATTACTGGAAATTTGGGTAATACGTTGTTGgaccgac                                                            >  1:410781/1‑251 (MQ=255)                                                                                                                                                                                                  gTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACTTATTACTGGAAATTTGGGTAATACGTTGTTGGACCGACCCGGTCTGGTTATCATATCGCGctct                                  >  1:447013/1‑251 (MQ=255)                                                                                                                                                                                                                             gTCTCCTCTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACTTATTACTGGAAATTTGGGTAATACGTTGTTGGACCGACCCGGTCTGGTTATCATATCGCGCTCTTAATTGCGGGAGGATGTAACATGAAc        <  2:257476/250‑1 (MQ=255)                                                                                                                                                                                                                                 cctcTGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACTTATTACTGGAAATTTGGGTAATACGTTGTTGGACCGACCCGGTCTGGTTATCATATCGCGCTCTTAATTGCGGGAGGATGTAACATGAACCTTg    >  1:372006/1‑250 (MQ=255)                                                                                                                                                                                                                                  ctctGCGCCGGTGACTGTATTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACTTATTACTGGAAATTTGGGTAATACGTTGTTGGACCGACCCGGTCTGGTTATCATATCGCGCTCTTAATTGCGGGAGGATGTAACATGAACCTTgac  >  1:154196/1‑251 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                         GTGATGTTGCCGGTTAGCGAAATTTTACCGAAAGCGGCCTATTATTTGATTCAGCGGCGTGATAGTCGCCAGACACCACTGACCGCGTCATTAATCACGCAATTCCGGCGAGAATGCGGCTATCTGCAAAGTTAAAACTGCATAAAAAAATAGAGTCTGTCGACATCCGCCAGACTCTACAGTACACACAGCAGTGCATCCGCGTCTTAAATCCGGCATTGTCTCCTCTGCGCCGGTGACTGTGTTATAACGGTTTTAACCTTTAGTTGCCAATTTTCTTCAGTGACAGATTTCACGAAAATATAAGTTACATTATTAATATCGTGAATGAATAATCATGCATAAGTATTTTGCTTAAAATATCGGCAATATTTGGAACTTATTACTGGAAATTTGGGTAATACGTTGTTGGACCGACCCGGTCTGGTTATCATATCGCGCTCTTAATTGCGGGAGGATGTAACATGAACCTTGAC  >  NC_000913/1405515‑1405990

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑