Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,689,817	C→A	9.1%	intergenic (+66/‑35)	manA → / → ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,689,817	0	C	A	9.1%	148.0 / 5.8	44	intergenic (+66/‑35)	manA/ydgA	mannose‑6‑phosphate isomerase/DUF945 family protein
Reads supporting (aligned to +/- strand):  ref base C (19/21);  new base A (2/2);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.64e-01

CTTAGTGATAAAGAAACCACCATTAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCAAGAAGATTGAAACCCATCTCGAAGACATGGTCGCGCAGGCGAACGCGCAACTCAAACTGACAGCTCCTGAATCCAACCTGGAAGTGAGTTATCAAAACTATCATCGCGGCGTATTCAGCAGCCAGTTGCAACTGTTGGTGAAACCCATTG  >  NC_000913/1689557‑1690080                                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                                        cTTAGTGATAAAGAAACCACCATTAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGAtt                                                                                                                                                                                                                                                           >  2:256375/1‑275 (MQ=255)                       tgagcacagcgagTGCCGCCAGTTTGTTCTGGCGCGAAGGGGAGGAAACGTTGTGGAAAGGTTCTCAACAGGCACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAACTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTAt                                                                                                                                                                                                                                     <  4:523435/265‑1 (MQ=255)                                    tGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGcc                                                                                                                                                                                                                                                                <  4:480239/235‑1 (MQ=255)                                    tGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGcc                                                                                                                                                                                                                                                                >  2:480240/1‑235 (MQ=255)                                    tGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTTTGGATAATCATTATGAATAAATCGCTg                                                                                                                                                                                                                        >  2:538167/1‑275 (MQ=255)                                                     gCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCAt                                                                                                                                                                                                       >  2:442083/1‑275 (MQ=255)                                                        tggaggggtaTGAAACGTTGTGGAAAGTNNNTAAGCATTTACAGCTTAAACCGGGTGAAACAGCCTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTTTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCAttg                                                                                                                                                                                                     <  3:148919/265‑1 (MQ=255)                                                                                aaGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAgg                                                                                                                                                                            <  1:35411/275‑1 (MQ=255)                                                                                    ttCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAggcggc                                                                                                                                                                        <  4:256374/275‑1 (MQ=255)                                                                                       tcggctgnaaaaGCTTAAACCGGGGGAATAAGCGTGTATTGCCGCCCAACAATAACCGGTGACTGTAAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATGAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCa                                                                                                                                                                     <  4:512274/264‑1 (MQ=255)                                                                                        cagcagTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTATCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCa                                                                                                                                                                     <  2:291258/274‑1 (MQ=255)                                                                                              ttACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCAttt                                                                                                                                                                                                                                                     >  2:565462/1‑188 (MQ=255)                                                                                                  aGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATg                                                                                                                                                                                                                                                 <  4:565461/188‑1 (MQ=255)                                                                                                                                                                   ggCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCAAGAAGATTGAAACCCATCTCGAAGACATGGTCGCGCAGGCGAACGCGCAACTCAAACTGACAg                                                                                         <  2:523616/275‑1 (MQ=255)                                                                                                                                                                                 tgtTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCGCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAAGCATTATGAATAAATGGGTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCAAGAAGATTGAAACCCATCTCGAAGACATGGTCGCGCAGGCGAACGCGCAACTCAAACTGACAGCTCCTGAATCCAAc                                                                           <  2:376228/275‑1 (MQ=255)                                                                                                                                                                                             gCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATCAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCAAGAAGATTGAAACCCATCTCGAAGACATGGTCGCGCAGGCGAACGCGCAACTCAAACTGCCAGCTCATGAAGTCAACCTGGCAGTGaa                                                                >  4:120803/1‑273 (MQ=255)                                                                                                                                                                                                 tAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCAAGAAGATTGAAACCCATCTCGAAGACATGGTCGCGCAGGCGAACGCGCAACTCAAACTGACAGCTCCTGAATCCAAcc                                                                          <  2:120804/260‑1 (MQ=255)                                                                                                                                                                                                         tACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCt                                                                                                                                                                                              >  4:560405/1‑136 (MQ=255)                                                                                                                                                                                                             gAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGc                                                                                                                                                                                          <  2:560406/136‑1 (MQ=255)                                                                                                                                                                                                                        cATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCAAGAAGATTGAAACCCATCTCGAAGACATGGTCGCGCAGGCGAACGCGCAACTCAAACTGACAGCTCCTGAATCCAACCTGGAAGTGAGTTATCAAAACTATCATCGCGGCGTATTc                                    >  2:360657/1‑275 (MQ=255)                                                                                                                                                                                                                          tctcTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATgg                                                                                                                                                                                                                                                <  7:135826/69‑1 (MQ=255)                                                                                                                                                                                                                          tctcTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATgg                                                                                                                                                                                                                                                >  8:135826/1‑69 (MQ=255)                                                                                                                                                                                                                                 cTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGa                                                                                                                                                                                                                                   >  6:1020205/1‑75 (MQ=255)                                                                                                                                                                                                                                 cTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGa                                                                                                                                                                                                                                   <  5:1020205/75‑1 (MQ=255)                                                                                                                                                                                                                                   aaGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATACTCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCt                                                                                                                                                                                   <  7:558992/121‑1 (MQ=255)                                                                                                                                                                                                                                   aaGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCt                                                                                                                                                                                   >  8:558992/1‑121 (MQ=255)                                                                                                                                                                                                                                     ncTTATTAAAGGCGTATAACACCTTCAGTCGGCCAGTCCGCCTGATTTCATTTTNTGGANAATAATTATGAATAAATCGCTGGNGGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCAAGAAGATTGAAACCCATCTCGAAGACATGGTCGCGCAGGCGAACGCGCAACTCAAACTGAc                                                                                           <  4:538166/206‑1 (MQ=255)                                                                                                                                                                                                                                        tattaAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAgg                                                                                                                                                                                           <  8:79367/108‑1 (MQ=255)                                                                                                                                                                                                                                        tattaAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAgg                                                                                                                                                                                           >  7:79367/1‑108 (MQ=255)                                                                                                                                                                                                                                        tattaAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCAAGAAGATTGAAACCCATCTCGAAGACATGGTCGCGCAGGCGAACGCGCAACTCAAACTGACAGCTCCTGAATCCAACCTGGAAGTGAGTTATCAAAACTATCATCGCGGCGTATTCAGCAGCCAGTTGCaa                     >  4:320148/1‑274 (MQ=255)                                                                                                                                                                                                                                              aGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCaagaag                                                                                                                                                   <  5:294110/142‑1 (MQ=255)                                                                                                                                                                                                                                              aGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCaagaag                                                                                                                                                   >  6:294110/1‑142 (MQ=255)                                                                                                                                                                                                                                                    ataACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTa                                                                                                                                                                                             >  2:334750/1‑94 (MQ=255)                                                                                                                                                                                                                                                       acacCTTCAGGCGGCCAGTCCGCCTGATTTCAtttt                                                                                                                                                                                                                                                    <  8:167932/36‑1 (MQ=255)                                                                                                                                                                                                                                                       acacCTTCAGGCGGCCAGTCCGCCTGATTTCAtttt                                                                                                                                                                                                                                                    >  7:167932/1‑36 (MQ=255)                                                                                                                                                                                                                                                       acacCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCAAGAAGATTGAAACCCAtctc                                                                                                                                    >  5:494691/1‑148 (MQ=255)                                                                                                                                                                                                                                                        cacCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCg                                                                                                                                                                                         <  4:334749/94‑1 (MQ=255)                                                                                                                                                                                                                                                           cTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTTCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCAAGAAGATTGAAACACATCTCGAAGACATGGTCGCGCAGGCCAACGCGCAACTCAAACTGACAGCTCCTGAATCCAACCTGGAAGTGAGGTATCAAACTGATCAGCGCGGCGTAATCACCAGCCAGTATCAACTGTTGGTGAAACACAttt  >  4:432751/1‑273 (MQ=255)                                                                                                                                                                                                                                                           cTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGc                                                                                                                                                         >  4:559336/1‑123 (MQ=255)                                                                                                                                                                                                                                                             tCAGGCGGACTGGCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATAc                                                                                                                                                             >  6:814021/1‑117 (MQ=255)                                                                                                                                                                                                                                                             tCAGGCGGACTGGCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATAc                                                                                                                                                             <  5:814021/117‑1 (MQ=255)                                                                                                                                                                                                                                                              cAGGCGGACTGGCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGc                                                                                                                                                                                                            <  6:217923/69‑1 (MQ=38)                                                                                                                                                                                                                                                              cAGGCGGACTGGCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGc                                                                                                                                                                                                            >  5:217923/1‑69 (MQ=38)                                                                                                                                                                                                                                                               aGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCaaga                                                                                                                                                     <  2:559337/123‑1 (MQ=255)                                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                                        CTTAGTGATAAAGAAACCACCATTAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGTGACTGTCAAAGGCCACGGCCGTTTAGCGCGTGTTTACAACAAGCTGTAAGAGCTTACTGAAAAAATTAACATCTCTTGCTAAGCTTATTAAAGGCTTATAACACCTTCAGGCGGCCAGTCCGCCTGATTTCATTTTATGGATAATCATTATGAATAAATCGCTGGTAGCGGTAGGCGTCATTGTTGCGCTAGGCGTAGTCTGGACAGGCGGCGCATGGTATACAGGCAAGAAGATTGAAACCCATCTCGAAGACATGGTCGCGCAGGCGAACGCGCAACTCAAACTGACAGCTCCTGAATCCAACCTGGAAGTGAGTTATCAAAACTATCATCGCGGCGTATTCAGCAGCCAGTTGCAACTGTTGGTGAAACCCATTG  >  NC_000913/1689557‑1690080

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑