Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,357,202	C→T	intergenic (‑92/+221)	sapA ← / ← ymjA	putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,357,202	0	C	T	96.8%	76.6 / ‑4.1	31	intergenic (‑92/+221)	sapA/ymjA	putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (16/14);  total (17/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.77e-01

CTTTGGATGGGTTAAAGGTGTTGACTTGCCCGCTGACGCAATAGACAAAACCGCTGTCGCGGATATCAGCATGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCCGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGATACTGACCGATCGTCTGCAATTAAATCATTACTCATTACCCCATTG  >  NC_000913/1356957‑1357440                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                               cTTTGGATGGGTTAAAGGTGTTGACTTGCCCGCTGACGCAATAGACAAAACCGCTGTCGCGGATATCAGCATGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCtgtgtg                                                                                                                                                                                                                                           >  1:148184/1‑251 (MQ=255)             tAAAGGTATTGACTTGCCCGCTGACGAAATCGACAAAACCGCTGTGGAGGATATCAGCATGCGGGGGCGCTTCAGCCGCGGAGATTGCCTGACCAATCACAAGTCCAGCAATCACCAAAAGAGACGAAAATACCTGGAGAATAATATTAAGGGGTTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCAATTACCGTTTGAGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTg                                                                                                                                                                                                                                >  2:57847/1‑250 (MQ=255)                    gtTGACTTGCCCGCTGACGCAATAGACAAAACCGCTGTCGCGGATATCAGCATGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTg                                                                                                                                                                                                                        <  2:272723/251‑1 (MQ=255)                                            gACAAAACCGCTGTCGCAGATATCAGCATGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACGCACAAGGCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGTGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGGGCAGGGGTCGTAATGAGGGCTGTGTGGTCGGTCGTTGAACAGGTGACGTCTCCATCTGTTCAACATTct                                                                                                                                                                                                <  2:136822/251‑2 (MQ=255)                                                           gcgGATATCAGCATGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTtctc                                                                                                                                                                                 <  1:189217/251‑1 (MQ=255)                                                                          cGGGGGAGATTCAGGCGCGGCGATGGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACAGTCGTACCCGTGATTTCTCTATAACTATAACTca                                                                                                                                                                  <  2:302648/251‑1 (MQ=255)                                                                                            ggcgATTGCCTGACCACTCACACGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCCGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGCTTTCTCTATAACTATAACTCACAGAACAACTTAGCgagg                                                                                                                                                >  2:223103/1‑251 (MQ=255)                                                                                                  tgcctgccCACTCACAAGTCCAGCAATCACCAAAAGAGACGATTACACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATGTGCCATTACCGGTGGTGTGCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACATGTGACGTCGCCACCTGTTCAACAGTCGTACCCGTGATTACGCTATAACTATAACTCACAGAACAACTTAg                                                                                                                                                     <  2:67135/240‑1 (MQ=255)                                                                                                  tGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAAAATTCGTACCCGTGATTTCTCTGTAACTATAACTCACAGAACAACTTAg                                                                                                                                                     >  1:67135/1‑240 (MQ=255)                                                                                                         ccccTCACAAGTCCAGCAATCACCAAAAGAGACGATAATTCCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTTCCATTACCGTGTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCAGCTGTTCAACATTCGTACCCGTGATTTCTctata                                                                                                                                                                             <  2:268886/206‑1 (MQ=255)                                                                                                         ccACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGAGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTctata                                                                                                                                                                             >  1:268886/1‑209 (MQ=255)                                                                                                              cacaAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGAt                                                                                                                                <  1:402393/249‑1 (MQ=255)                                                                                                                                 aaaaGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGc                                                                                                            >  1:453121/1‑250 (MQ=255)                                                                                                                                     aagaCGATAATCCCTGGCGCATAATATTAAGGGATTGTATGTAAAGAGTCTATCTTACTAATATTTAATGACATTTGGCATTACCGTTTGTGTGCAGGGGTCGGAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCt                                                                                                       <  2:2255/250‑1 (MQ=255)                                                                                                                                                       gcATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGtt                                                                                     >  1:444657/1‑251 (MQ=255)                                                                                                                                                             tattaggggagtttgtataccgagGCTATCTTACTAATATTTAATGACATTGGCCATTACCGTTTGAGTTCAGGGGTCGTAATGAGAGCTGTGTAGTTGATCGTTGAACTGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATCACTCTAACTCACAAACCAACTTAGCGAGGAGCAAAGCGGTACGATCGTGAGAAACCAATTTAAGCGCGCTTCAGTGCGTGTCATTGTTAGCCa                                                                                >  2:6833/22‑250 (MQ=255)                                                                                                                                                               ttAAGGGATTTTATGTAAAGAGGCTATCTTACTCATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGCGGAGCAGAGCGGTACGATCGTGAGAAACCATTTAAAGCACGCTGCAGTGCGTGTCATTGTTAGcc                                                                                 >  2:241021/1‑247 (MQ=255)                                                                                                                                                                tAAGGGATTTTATGTAAAGAGGCTATCTTTCTAATATTTAATGACATTTGCCATTACCGGTTGTGTGCAGTGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGTGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATGGTTAGCCAGAt                                                                             <  2:305199/250‑1 (MQ=255)                                                                                                                                                                 aaGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATgc                                                                           >  1:448494/1‑251 (MQ=255)                                                                                                                                                                           aTGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGAGTGCACg                                                                 >  2:395367/1‑251 (MQ=255)                                                                                                                                                                              tAAAGAGGCTATCTTACTAATATATAATGACATTTGCCATTACCGTTTGTGTTCCGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGGACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCAGGGAGCAGAGCAGTAAGATCGTGAGAAACCCTTTCAAGCACTCTGCAGTGCGTGTCATTGTTAGACAGATGCGGCGTGAACGCtt                                                              >  2:402887/1‑251 (MQ=255)                                                                                                                                                                               caaaagGCTATCTTACTAATATTTAATTACATCTGCCATTACCGGTTGTATTCAGGTGTCGTAATGAGGGCTGTGTGGTTAGTCGTTGAACAGTTGACGTCGCCGTCTGTTCAACATTCGTACCCGTGGTTTCTCTATAACTATAACTCACAGAACAACTTAGCGCGGAGCCGAGCGGTACGATCGTGTACAACCCATTAACTAACGCTGCAGTGCGTGTACTTGTTTGCAAGATGCGGCGTgcaggctgt                                                             >  2:12532/5‑243 (MQ=255)                                                                                                                                                                                aaGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTa                                                            <  2:126789/251‑1 (MQ=255)                                                                                                                                                                                 agagGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTAACCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTAt                                                           >  1:167703/1‑251 (MQ=255)                                                                                                                                                                                   gggCTCTCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTTTTCAGGGGTCGTAATGATGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCATAGCGTTACGATCGTGAGAAACCCATTAAAGCACGCTTCAGTTCGTGTCATTGTTAGCCAGAGGCGGCGTGAACGCTTTATcc                                                         <  2:268504/250‑1 (MQ=255)                                                                                                                                                                                                     tgaatggcaattGCCATGACCGTTTGTGTTCAGGGGTCGTAATGAGGGATGTGTGGTTGGTCGTGGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGAGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGATACTGAcc                                        <  2:207227/240‑1 (MQ=255)                                                                                                                                                                                                       aaTGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTTTCCGGACAACGATACTGACCGAt                                     >  2:218070/1‑251 (MQ=255)                                                                                                                                                                                                         taaCATTTGCCATTACCGATTGTGTTCAGGGGTCTTAATGAGGGCTGTGGGGTTGGTCGTTGAACAGGTGACGTAGCCATCTGTTCAACATTCGTACCCGTGATTTATCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCGGAGCGGTACGATCGTGAGCAGCCCATTAAAGCACGATGCAGTGCGTGGCATTGGTAGCCAGATGCGGAGTGAACGCTTTATCCGGACAACGATagtgtccactcg                                   >  2:85791/3‑240 (MQ=255)                                                                                                                                                                                                                        ccgtgtggtttCAGGGGGCGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGGGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGTACATCTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCTGACAACGATACTGACCGATCGTCTGCAATTAAAtca                    <  2:281575/242‑1 (MQ=255)                                                                                                                                                                                                                                        gtaggaaTGAGGGCTGTGTGGTTGGTCGTTGAACAGGGGACGTCGCCATCTGTTCAACATTCGTTCCCGTGAATTCGCTATAACTATAACTCACAGAACAACGTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGGCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGATACTGACCGATCGTCTGCAATTAAATCATTACTCATTACCCCAt    <  2:156469/246‑1 (MQ=255)                                                                                                                                                                                                                                          cGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGATACTGACCGATCGTCTGCAATTAAATCATTACTCATTACCCCATTg  >  2:147140/1‑251 (MQ=255)                                                                                                                                                                                                                                          cGTAATGAGGGCTGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGATACTGACCGATCGTCTGCAATTAAATCATTACTCATTACCCCATTg  >  1:185145/1‑251 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                               CTTTGGATGGGTTAAAGGTGTTGACTTGCCCGCTGACGCAATAGACAAAACCGCTGTCGCGGATATCAGCATGCGGGGGAGATTCAGGCGCGGCGATTGCCTGACCACTCACAAGTCCAGCAATCACCAAAAGAGACGATAATACCTGGCGCATAATATTAAGGGATTTTATGTAAAGAGGCTATCTTACTAATATTTAATGACATTTGCCATTACCGTTTGTGTTCAGGGGTCGTAATGAGGGCCGTGTGGTTGGTCGTTGAACAGGTGACGTCGCCATCTGTTCAACATTCGTACCCGTGATTTCTCTATAACTATAACTCACAGAACAACTTAGCGAGGAGCAGAGCGGTACGATCGTGAGAAACCCATTAAAGCACGCTGCAGTGCGTGTCATTGTTAGCCAGATGCGGCGTGAACGCTTTATCCGGACAACGATACTGACCGATCGTCTGCAATTAAATCATTACTCATTACCCCATTG  >  NC_000913/1356957‑1357440

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑