Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,997,620	C→T	7.5%	intergenic (‑20/+72)	insC1 ← / ← ygeQ	IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,997,620	0	C	T	7.5%	161.4 / 2.3	53	intergenic (‑20/+72)	insC1/ygeQ	IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant
Reads supporting (aligned to +/- strand):  ref base C (28/21);  new base T (2/2);  total (30/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTT  >  NC_000913/2997491‑2997768                                                                                                                                  |                                                                                                                                                     cgcgctgataagttacctcctgaccatcaatgagaattaaaacacgggaggatgcttcgccactagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtCTAAAAACTAGTATTAAGAc                                                                                                                                   <  5:29892‑M2/20‑1 (MQ=255)                                                           tttCCTGTGTGGTACGACGTCTGCGTTTCTGCTGCGCTAATACTTCAATAATCTGTTCTCCAATGACTAGTCTAAAAACTAGTTTTAAGTCTATCACTTATTTAAGTTATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTg                                                                         <  2:254526/149‑1 (MQ=11)                                                                  tgtgGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCtt                                                                    <  3:314045/147‑1 (MQ=35)                                                                       tACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTtcttct                                                             >  8:66554/1‑149 (MQ=255)                                                                       tACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTtcttct                                                             <  4:345915/149‑1 (MQ=255)                                                                       tACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTtcttct                                                             >  2:34927/1‑149 (MQ=255)                                                                           cctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtTTTTAGACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTgg                                                                                                   >  8:337357‑M2/56‑107 (MQ=255)                                                                           cctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtTTTTAGACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTgg                                                                                                   <  7:337357‑M2/52‑1 (MQ=255)                                                                           ccGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGgtg                                                         <  6:211628/149‑1 (MQ=255)                                                                           ccGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGgtg                                                         >  5:272098/1‑149 (MQ=255)                                                                            cGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGgtgt                                                        >  7:350326/1‑149 (MQ=255)                                                                              tCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGtt                                                       >  3:155574/1‑148 (MQ=255)                                                                                tGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAACTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTAt                                                    >  4:210843/1‑149 (MQ=255)                                                                                  cGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTACTGGTGTTTATCt                                                  <  2:195458/149‑1 (MQ=255)                                                                                    tttCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCttt                                                >  5:72105/1‑149 (MQ=255)                                                                                           ggCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGAt                                         >  6:259401/1‑149 (MQ=255)                                                                                             cactcaGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGAttt                                       <  6:101059/144‑1 (MQ=255)                                                                                               cTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGt                                     >  3:28163/1‑149 (MQ=255)                                                                                               cTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGt                                     <  7:66554/149‑1 (MQ=255)                                                                                                 aaGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTg                                                            <  6:67764/124‑1 (MQ=255)                                                                                                 aaGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTg                                                            >  5:67764/1‑124 (MQ=255)                                                                                                  aGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTa                                    <  1:390920/147‑1 (MQ=255)                                                                                                  aGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTa                                    <  7:23485/147‑1 (MQ=255)                                                                                                  aGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAgg                                  <  6:272098/149‑1 (MQ=255)                                                                                                      atcaatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCttt                                                <  6:327410/131‑1 (MQ=255)                                                                                                      atcaatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCttt                                                >  5:327410/1‑131 (MQ=255)                                                                                                      atcaatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGata                               >  4:316446/1‑148 (MQ=255)                                                                                                      atcaatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGata                               >  5:366347/1‑148 (MQ=255)                                                                                                       tcaatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                             >  1:189061/1‑149 (MQ=255)                                                                                                       tcaatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                             >  5:343640/1‑149 (MQ=255)                                                                                                       tcaatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                             >  5:117967/1‑149 (MQ=255)                                                                                                        caatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                             >  5:66835/1‑148 (MQ=255)                                                                                                         aatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaat                            >  5:300848/1‑148 (MQ=255)                                                                                                          atcatcTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaataa                          <  5:70423/149‑1 (MQ=255)                                                                                                           tcatcTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAAc                         <  3:316446/149‑1 (MQ=255)                                                                                                                  ttCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACAtt                      <  5:144162/145‑1 (MQ=255)                                                                                                                  ttCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAg                   <  6:300848/148‑1 (MQ=255)                                                                                                                    ctcCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                             >  3:180810/1‑136 (MQ=255)                                                                                                                    ctcCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                             <  4:180810/136‑1 (MQ=255)                                                                                                                     tcttaatactagtTTTTAGACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTCGAGATTCAGGGGGCCAGt                                                                                  >  5:312248‑M2/14‑82 (MQ=255)                                                                                                                     tcttaatactagtTTTTAGACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTCGAGATTCAGGGGGCCAGt                                                                                  <  6:312248‑M2/69‑1 (MQ=255)                                                                                                                     tcCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTa                 >  4:271649/1‑147 (MQ=255)                                                                                                                       cAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGc             >  3:164855/1‑149 (MQ=255)                                                                                                                       cAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAACTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGGCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGc             <  4:269013/149‑1 (MQ=255)                                                                                                                          tGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCg           >  2:13380/1‑148 (MQ=255)                                                                                                                              tagtCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAATCTTGCTCTTTTCTTATGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAATTAAAGCCGCAtct      >  3:222533‑M2/5‑148 (MQ=255)                                                                                                                              tagtCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCg      >  1:276820‑M2/5‑149 (MQ=255)                                                                                                                              tagtCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCg      >  3:99368‑M2/5‑149 (MQ=255)                                                                                                                              tagtCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCg      >  7:28678‑M2/5‑149 (MQ=255)                                                                                                                                gtCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGc    >  2:35397‑M2/3‑149 (MQ=255)                                                                                                                                 tCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCt   <  2:189061‑M2/148‑1 (MQ=255)                                                                                                                                 tCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCt   >  7:268191‑M2/2‑149 (MQ=255)                                                                                                                                 tCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCt   <  5:337326‑M2/148‑1 (MQ=255)                                                                                                                                  cTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCtt  >  1:237833/1‑149 (MQ=255)                                                                                                                                  cTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTCGAGATTCAGGGGGCCAGTCTAAACTTGCACTTTTCTTCTGGTGGTTATCTTTGAAAGATTTGTAGGATTAATAACATTAAGTAAAGCCGGATCGGcat  >  6:116696/1‑147 (MQ=25)                                                                                                                                  |                                                                                                                                                     CGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTT  >  NC_000913/2997491‑2997768

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑