Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,313,074	(A)7→8	intergenic (‑83/‑276)	alsR ← / → rpiB	DNA‑binding transcriptional repressor AlsR/allose‑6‑phosphate isomerase/ribose‑5‑phosphate isomerase B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,313,074	1	.	A	84.2%	54.7 / 3.0	19	intergenic (‑83/‑276)	alsR/rpiB	DNA‑binding transcriptional repressor AlsR/allose‑6‑phosphate isomerase/ribose‑5‑phosphate isomerase B
Reads supporting (aligned to +/- strand):  ref base . (3/0);  new base A (5/11);  total (8/11)
Fisher's exact test for biased strand distribution p-value = 5.78e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

TTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAA‑TAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCATTTAATTAGTTTAAAAACATGATGTTATTTGTTTTTCTGGTTTTTTAGATGATAGATGTTGCTGGATGGTGAGTGTCTTTAACGCTATTGCGCTGTCAGATGTAACTCTGTAAAACAGATCAGGAAGGCGTAATTCATCGATTTTGGGTGTTTTTAATTCATTAACATCACAAATGTTTTTTG  >  NC_000913/4312827‑4313317                                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                    ttCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGCAAAGATGCTGGCGACTTCACa‑aa‑aaaaat                                                                                                                                                                                                                                                    >  2:171502/1‑248 (MQ=255)            ctatAATTGCGGGTGCACACCTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATAACCACAGCAAGAACAGAAAAGATGCTGGCGACTTACCA‑AACAAAA‑TAAAATTTATaa                                                                                                                                                                                                                                         >  2:334614/4‑250 (MQ=255)                   tGCGGGTGCACAACTCAGGTTACCGGGTTTGAGGAACCACGCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTGCATTCGCAGGTAAGGCGCTAACCCTAAACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAAATAAAATTTATAAAGtttat                                                                                                                                                                                                                                  <  1:27444/250‑1 (MQ=255)                    gCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAAATAAAATTTATAAAGtttatt                                                                                                                                                                                                                                 <  1:389968/250‑1 (MQ=255)                     cGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAAATAAAATTTATAAAGtttatttt                                                                                                                                                                                                                               >  1:57001/1‑251 (MQ=255)                                        aCCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAAATAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGt                                                                                                                                                                                                            <  1:69245/251‑1 (MQ=255)                                                      aCCACTCAACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAAATAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAAtttt                                                                                                                                                                                               >  1:339884/1‑250 (MQ=255)                                                            ccACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAAATAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCAt                                                                                                                                                                                        <  2:131421/251‑1 (MQ=255)                                                            ccACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGAAAGGCGCTAACACTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGATCTCTTGTCCTTGAATTGAAGAAGCCACTATATCACCACAGCAGGAACAGAAAAGATGCTGGCGACTTCACA‑AACAAAA‑TAAAATTTATAAAGTTTATTTTATTGTGACCAATGACGAGGGGCTTAAAATTTTATTTCAt                                                                                                                                                                                        >  2:256485/1‑251 (MQ=255)                                                             cACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAAATAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCAtt                                                                                                                                                                                       <  1:248082/251‑1 (MQ=255)                                                                                     cATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACACAA‑AAAA‑TAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCATTTAATTAGTTTAAAAACATGATGtt                                                                                                                                                               >  2:361255/1‑251 (MQ=255)                                                                                                     aTTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAAATAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCATTTAATTAGTTTAAAAACATGATGTTATTTGTTTTTCTGGtt                                                                                                                                               <  1:361255/251‑1 (MQ=255)                                                                                                                         cccTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAAATAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCATTTAATTAGTTTAAAAACATGATGTTATTTGTTTTTCTGGTTTGTTAGATGATAGATGTTGc                                                                                                                           <  1:309504/251‑1 (MQ=255)                                                                                                                                    tCGGAAGCG‑TGTAATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACGATAGCACCACAGCAAGAACAGAAAAGATGCTGTCGACTTCACA‑AA‑AAAAATAAAATTGATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTTATTTAATTAGTGTAAAAACAGGATGTTATTTGTTTTTCTTGTTTTTTAGAGGATAGATGTCGCTGGATGGTGa                                                                                                                 <  2:103450/250‑1 (MQ=255)                                                                                                                                                                  cTCATCTCGTTCTCTTGTCCTTGAATTGACGACGCCACTATATCACCACAGCAAGAACAGAAAAGCTGCTGGCGACTTCCCA‑AA‑AAAAATAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCATTTAATTAGTTTAAAAACATGATGTTATTTGTTTTTCTGGTTTTTTAGATGATAGATGTTGCTGGATGGTGAGTGTCTTTAACGCTATTGCGCTGTCAGATg                                                                                   >  2:77412/1‑251 (MQ=255)                                                                                                                                                                               ctTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAAATAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCATTTAATTAGTTTAAAAACATGATGTTATTTGTTTTTCTGGTTTTTTAGATGATAGATGTTGCTGGATGGTGAGTGTCTTTAACGCTATTGCGCTGTCAGATGTAACTCTGTaaa                                                                       >  1:346914/1‑250 (MQ=255)                                                                                                                                                                                                        tataTCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAAATAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCATTTAATTAGTTTAAAAACATGATGTTATTTGTTTTTCTGGTTTTTTAGATGATAGATGTTGCTGGATGGTGAGTGTCTTTAACGCTATTGCGCTGTCAGATGTAACTCTGTAAAACAGATCAGGAAGGCGTAATTCa                                                <  2:206155/248‑1 (MQ=255)                                                                                                                                                                                                        tataTCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAAATAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCATTTAATTAGTTTAAAAACATGATGTTATTTGTTTTTCTGGTTTTTTAGATGATAGATGTTGCTGGATGGTGAGTGTCTTTAACGCTATTGCGCTGTCAGATGTAACTCTGTAAAACAGATCAGGAAGGCGTAATTCa                                                >  1:206155/1‑248 (MQ=255)                                                                                                                                                                                                                              aaaaGATGCTGGCGACTTCACA‑AA‑AAAAATTAAATTTATAAAGTTGATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCATTTAATTAGTTTAAAAACATGATGTTATTTGTTTTTCTGGTTTTTTAGATGATAGATGTTGCTGGATGGTGAGTGTCTTTAACGCTATTGCGCTGTCAGATGTAACTCTGTAAAACAGATCAGGAAGGCGTAATTCATCGATTTTGGGTGTTTTTAATTCAt                       <  2:352806/251‑1 (MQ=255)                                                                                                                                                                                                                                         gCGACTTCACA‑AA‑AAAAATAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCATTTAATTAGTTTAAAAACATGATGTTATTTGTTTTTCTGGTTTTTTAGATGATAGATGTTGCTGGATGGTGAGTGTCTTTAACGCTATTGCGCTGTCAGATGTAACTCTGTAAAACAGATCAGGAAGGCGTAATTCATCGATTTTGGGTGTTTTTAATTCATTAACATCACaa            <  1:313243/251‑1 (MQ=255)                                                                                                                                                                                                                                                  aa‑aa‑aaaa‑TAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCATTTAATTAGTTTAAAAACATGATGTTATTTGTTTTTCTGGTTTTTTAGATGATAGATGTTGCTGGATGGTGAGTGTCTTTAACGCTATTGCGCTGTCAGATGTAACTCTGTAAAACAGATCAGGAAGGCGTAATTCATCGATTTTGGGTGTTTTTAATTCATTAACATCACAAATGTTTTTTg  <  2:326529/250‑1 (MQ=255)                                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                    TTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTG‑AATCAAACTCTGACTGGCTCATCACGTTCTCTTGTCCTTGAATTGAAGACGCCACTATATCACCACAGCAAGAACAGAAAAGATGCTGGCGACTTCACA‑AA‑AAAA‑TAAAATTTATAAAGTTTATTTTATTGTGAACAATGGCGAGTGGCTTAAAATTTTATTTCATTTAATTAGTTTAAAAACATGATGTTATTTGTTTTTCTGGTTTTTTAGATGATAGATGTTGCTGGATGGTGAGTGTCTTTAACGCTATTGCGCTGTCAGATGTAACTCTGTAAAACAGATCAGGAAGGCGTAATTCATCGATTTTGGGTGTTTTTAATTCATTAACATCACAAATGTTTTTTG  >  NC_000913/4312827‑4313317

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑