Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_010473	1,386,237	2 bp→GT	intergenic (‑60/+16)	lacI ← / ← mhpR	DNA‑binding transcriptional repressor LacI/DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_010473	1,386,237	0	T	G	97.2%	139.0 / NA	37	intergenic (‑60/+17)	lacI/mhpR	DNA‑binding transcriptional repressor LacI/DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (1/0);  major base G (17/18);  minor base A (1/0);  total (19/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	NC_010473	1,386,238	0	G	T	97.3%	132.9 / ‑5.6	37	intergenic (‑61/+16)	lacI/mhpR	DNA‑binding transcriptional repressor LacI/DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base T (18/18);  minor base C (1/0);  total (19/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

TTTTTCCCGCGTTTTCGCAGAAACGTGGCTGGCCTGGTTCACCACGCGGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑TGCGCCATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGTTCAATGGTCATTGCGCTCGCCATATACACCAGATTCAGACAGCCAATCAC  >  NC_010473/1386067‑1386421                                                                                                                                                                                   ||                                                                                                                                                                                            tttttCCCGCGTTTTCGCAGAAACGTGGCTGGCCTGGTTCACCACGCGGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCT‑CCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAa‑tgca                                                                                                                                                             >  1:27182S95/1‑200 (MQ=255)  ttttCCCGCGTTTTCGCAGAAACGTGGCTGGCCTGGTTCACCACGCGGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGG‑CGTC‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAa‑tgcat                                                                                                                                                            <  1:3428S4/200‑1 (MQ=255)        cgcgTTTTCGCAGAAACGTGGCTGGCCTGGTTCACCACGCGGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGc                                                                                                                                                       <  1:18213S33/200‑1 (MQ=255)          cgTTTTCGCAGAAACGTGGCTGGCCTGGTTCACCACGCGGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCtt                                                                                                                                                     >  1:75S15/1‑200 (MQ=255)              ttCGCAGAAACGTGGCTGGCCTGGTTCACCACGCGGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACAT‑CACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCt                                                                                                                                                >  1:32009S36/1‑200 (MQ=255)                 gCAGAAACGTGGCTGGCCTGGTTCACCACGCGGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑ACT‑‑‑CAATCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCgg                                                                                                                                           <  1:31479S11/200‑1 (MQ=255)                                  cTGGTTCACCACGCGGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGcc                                                                                                                             >  1:4460S4/1‑200 (MQ=255)                                        caccacGCGGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTGAATTAATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGTAGAACGTGA‑‑TCCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTg                                                                                                                           >  1:23064S12/1‑200 (MQ=255)                                        caccacGCGGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGAt                                                                                                                       >  1:7333S27/1‑200 (MQ=255)                                           cacGCGGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCa                                                                                                                    >  1:16188S2/1‑200 (MQ=255)                                            acGCGGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCaa                                                                                                                   >  1:1041S137/1‑200 (MQ=255)                                             cgcgGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑c                                                                                                                 <  1:26449S23/200‑1 (MQ=255)                                                    aaCGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATCGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCcttct                                                                                                          <  1:12960S54/200‑1 (MQ=255)                                                     aCGGTCTGATATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCGAGCGTC‑GATGGTGT‑CAACGTAAA‑T‑AGTGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCcttct                                                                                                          >  1:6368S14/1‑200 (MQ=255)                                                        gTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGa                                                                                                      >  1:26826S35/1‑200 (MQ=255)                                                        gTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCT‑CCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGAt                                                                                                     >  1:15500S9/1‑200 (MQ=255)                                                            g‑‑ATAATAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTg                                                                                                  <  1:19036S27/200‑1 (MQ=255)                                                                     gaCACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTA‑‑‑‑AAATAACTCT‑‑‑‑‑GGGCGCT‑ATCATGCCATACCGCCAGCGGCTT‑ATCAACATTCAGATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTAccc                                                                                       >  1:22529S51/1‑200 (MQ=255)                                                                       cacCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTAc                                                                                         <  1:2162S11/200‑1 (MQ=255)                                                                                       gACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGa                                                                         <  1:3372S25/200‑1 (MQ=255)                                                                                        aCATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGG‑CGTC‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAg                                                                       <  1:5867S3/200‑1 (MQ=255)                                                                                                  aCGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGTATCAA‑CCC‑‑‑CTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGc                                                           <  1:6412S1/200‑1 (MQ=255)                                                                                                          ggTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCGT‑CCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTg                                                     >  1:3180S21/1‑200 (MQ=255)                                                                                                           gTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTg                                                     >  1:15533S14/1‑200 (MQ=255)                                                                                                            tttCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑CTCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGt                                                    <  1:25727S9/200‑1 (MQ=255)                                                                                                             atagcaTTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCTCATGCTTAGATACCGCGAAAGGTTTGTCCAACATTC‑GATGGTGTTAAACGTAAA‑T‑CATGC‑GCTTCGCCT‑CCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGtt                                                   >  1:27645S2/5‑200 (MQ=255)                                                                                                                acaTTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTC‑ATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGTTCAAt                                               <  1:15963S5/200‑1 (MQ=255)                                                                                                                acaTTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGC‑ACT‑CGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCC‑‑‑AGATGCTTTTCCGCTGCCTGTTCAATGGTc                                           >  1:25109S6/1‑200 (MQ=255)                                                                                                                 caTTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGTTCAAt                                               >  1:1338S20/1‑200 (MQ=255)                                                                                                                    tCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGTTCAATGGt                                            <  1:14858S7/200‑1 (MQ=255)                                                                                                                                      tGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTTGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGTTCAATGGTCATTGCGCTCGCCa                              <  1:14980S13/200‑1 (MQ=255)                                                                                                                                          tctctTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGAAAAATGCATGCCGCTTCGC‑TTTCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGTTCAATGGTCATTGCGCTCGCCAtata                          <  1:81S24/200‑1 (MQ=255)                                                                                                                                           tcctTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑CTCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCCGGTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGTTCAATGGTCATTGCGCTCGCCATATac                         <  1:1058S16/198‑1 (MQ=255)                                                                                                                                           ctctTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGTTCAATGGTCATTGCGCTCGCCATATac                         >  1:1959S39/1‑200 (MQ=255)                                                                                                                                                            cATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAAACCCCTTCTTCAATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGTTCAATGGTCATTGCGCTCGCCATATACACCAGATTCAGACAg          >  1:16423S8/1‑200 (MQ=255)                                                                                                                                                            cATGCCATACCGCGAAAGGTTT‑GTCAACATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGTTCAATGGTCATTGCGCTCGCCATATACACCAGATTCAGACAGc         <  1:2039S149/200‑1 (MQ=255)                                                                                                                                                                   tACCGCGAAAGGTTT‑GTCAACATTC‑AATGGCGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGTTCAATGGTCATTGCGCTCGCCATATACACCAGATTCAGACAGCCAATCAc  <  1:16430S12/200‑1 (MQ=255)                                                                                                                                                                                   ||                                                                                                                                                                                            TTTTTCCCGCGTTTTCGCAGAAACGTGGCTGGCCTGGTTCACCACGCGGGAAACGGTCTG‑‑ATAAGAGACACCGGCATACTCTGCGACATCGTATAACGTTACTGGTTTCACATTCACCACCCTG‑‑‑‑AATTGACTCTCTTCCGGGCGCT‑ATCATGCCATACCGCGAAAGGTTT‑TGCGCCATTC‑GATGGTGT‑CAACGTAAA‑TGCATGCCGCTTCGCCTTCCGGCCACCAGAATAGCCTGCGATTCAA‑CCCCTTCTTCGATCTGTTTTGCTACCCGTTGTAGCGCCGGAAGATGCTTTTCCGCTGCCTGTTCAATGGTCATTGCGCTCGCCATATACACCAGATTCAGACAGCCAATCAC  >  NC_010473/1386067‑1386421

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 48 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑