Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	5,159	0	G	A	44.9%	47.5 / 25.2	49	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (24/3);  new base A (0/22);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 5.18e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGA  >  NC_000913/5013‑5307                                                                                                                                                       |                                                                                                                                                     atcaGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATa                                                                                                                                                  <  1:528200/151‑1 (MQ=255)        aaaTCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATaacaa                                                                                                                                              >  1:18958/1‑148 (MQ=255)        aaaTCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAAccg                                                                                                                                           >  1:303898/1‑151 (MQ=255)         aaTCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAAccgc                                                                                                                                          >  1:457199/1‑151 (MQ=255)             tATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGtt                                                                                                                                      >  1:301441/1‑151 (MQ=255)                   ttATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATc                                                                                                                                >  1:16692/1‑151 (MQ=255)                       ctcAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGCTCTCATCGAGt                                                                                                                            >  2:363342/1‑151 (MQ=255)                           aTCAGGCCGGGGTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTACGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAAt                                                                                                                         >  1:221686/1‑150 (MQ=255)                               ggCGGGGTTTGTTTTTATGCACCCCGGTTTTTTTATAAAAAAATTAGGGAAAAAAATGAAAGGAAAAAAGGAAAAA‑TTCACAAAAAAGG‑CGTTACCT‑TAAAGATTAGGA‑TGGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCg                                                                                                                    <  2:397522/151‑1 (MQ=255)                               ggCGGGGTTTGTTTTTAGGCAGCCCGGTTTTTTTATGAAAAAATTATGAAAAAAAATGAGAGGAAAAAAGGAGAAA‑TTCTAAATAAATG‑CGTTATCT‑TAGATATAAGGA‑TGGCGGAGAAAAACAGCCGCCGTTCTCATCGAGTAATCTcc                                                                                                                     <  1:236531/150‑1 (MQ=255)                               ggCCGGGTTTGTTTTTAGGCAGCCGGGTTTTTTTAAGAAAAAATTATGAAAAAAAATGACAGGAAAAAAGGAAAAA‑TTCTCAAAAATGG‑CGGTAACT‑AAGAGATTAGGA‑TTGCGGAAAATAACAACCGCCGTTCTCATCGAGTAAtctc                                                                                                                      <  2:427543/149‑1 (MQ=255)                                 ccGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCgg                                                                                                                   >  2:196980/1‑150 (MQ=255)                                          cTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAccc                                                                                                         >  1:712969/1‑151 (MQ=255)                                                   aGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGc                                                                                                >  1:666321/1‑151 (MQ=255)                                                    gCCCGGTTTTTTTAAAAAAAAATTAGGGAAAAAAATGACAGGGAAAAAGGAAAAT‑TTCTCAATAATGG‑GGGTAATT‑TAAAGATTAGGA‑TGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATaa                                                                                                     <  2:82928/145‑1 (MQ=255)                                                     cccGGTTTTTTTATGAAAAAATTATGGAAAAAAAGGACGGGAAAAAAGGAAAAA‑TTCTAAATAAGGG‑GGGTACTT‑TAGAGATAAGGA‑TTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCa                                                                                               <  2:655001/150‑1 (MQ=255)                                                        ggCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATg                                                                                            >  2:603685/1‑150 (MQ=255)                                                              tttaaaaaaaaaTTAGGGAAAAAAATAAAAGGAAAAAAGGAAAAA‑TTCTAAATAAATG‑CGGTAACT‑AAGAGATAAGAT‑TTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATaaaa                                                                                      <  2:702528/141‑1 (MQ=255)                                                                tATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAgg                                                                                    >  2:207109/1‑150 (MQ=255)                                                                    aagaaATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTa                                                                                >  1:459554/1‑150 (MQ=255)                                                                    aaaaaaTTAGGAAAAAAAATGACAGGAAAAAAGAAAAAA‑TTCTAAATAAAGG‑CGGTAACT‑TAGAGATTAGGA‑TGGCGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGa                                                                                   <  1:243789/144‑1 (MQ=255)                                                                      gaaATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAAcc                                                                             >  1:128130/1‑151 (MQ=255)                                                                        aaTTATGAAAAAAAATGACAGGAAAAAAGAAAAAA‑TTCTAAAAAAAGG‑CGTTAACT‑TAGAGATTAGGA‑TGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtg                                                                           <  2:88273/151‑1 (MQ=255)                                                                          ttATGGAAAAAAATGACGGAAAAAAAGAAAAAA‑TTCTAAAAAAATG‑CGATAACT‑TAGAGATTGGGT‑TGGGGAAAAAAAACACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgt                                                                          <  1:685870/150‑1 (MQ=255)                                                                            aTGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGa                                                                        >  2:481227/1‑150 (MQ=255)                                                                             tGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaa                                                                       >  2:387689/1‑150 (MQ=255)                                                                              ggAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaa                                                                      >  2:599497/1‑150 (MQ=255)                                                                               gagaAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaaa                                                                     >  1:350230/1‑150 (MQ=255)                                                                                agaAAAATGACGGGGAAAAGGGAAAAA‑TTCT‑AAAAAAAG‑CGGTTATTATGGAGATGGGAA‑TGGGGGAAAATACCAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaa                                                                      <  2:609154/148‑1 (MQ=255)                                                                                 aaaaaaGGAAAGGAAAAAAGGAGAAA‑TTCTAAATAAAGG‑CGGTAACT‑GAGAGATTAGAA‑CGGCGGAGAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGa                                                                  <  1:575375/150‑1 (MQ=255)                                                                                  aaaaaTGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaaa                                                                     >  1:74041/1‑147 (MQ=255)                                                                                  aaaaaTGAC‑GGAAAAAAGGAAAAATTTCTCAA‑AAATGCCGGAAACT‑AAGAAATTAGTA‑TCGCGAAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGAt                                                                 <  2:533929/151‑1 (MQ=255)                                                                                    aaaTGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGc                                                               >  2:323560/1‑151 (MQ=255)                                                                                          aagaaaaaaaGGAAAAA‑TCCTCAAAAAAGG‑CGTTAACT‑TAGAGATTAGGA‑TGGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTa                                                         <  1:1663/146‑1 (MQ=255)                                                                                            ggaaaaaaGGAAAAA‑TTCTAAAAAAAGG‑CGGTAACT‑TAGAGATTAGGA‑TGGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTa                                                         <  2:214411/146‑1 (MQ=255)                                                                                               aaaaaGGAAAAA‑TTCAAAAAAAAGG‑CGGTAACT‑TAGAGATTAGGA‑TGGGGAAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATc                                                       <  2:166329/148‑1 (MQ=255)                                                                                                 aaaGGAAAAA‑TTCAAAATAAATG‑CGTTAATT‑TAGAGTTAAGGT‑TTGGGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACt                                                  <  1:591169/151‑1 (MQ=255)                                                                                                    ggAAAAA‑TTCTAAAAAAAGG‑CGTAAACT‑AAGAGATTGGGA‑TGGCGGAAAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGc                                               <  2:79678/151‑1 (MQ=255)                                                                                                         aa‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACttt                                          >  1:361586/1‑151 (MQ=255)                                                                                                                 aaaaaaTG‑CGGTAACT‑TAGAAATTAGGA‑TTGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCt                                      <  2:16693/145‑1 (MQ=255)                                                                                                                 aaTAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGt                                   >  2:163688/1‑151 (MQ=255)                                                                                                                 aaTAAAGG‑CGTTAACT‑AAGATATTAGGT‑TGGCGGAAAATACCACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTcc                                        <  2:312715/146‑1 (MQ=255)                                                                                                                  aaaaaagccgttAACT‑AAGATA‑TAGGATTTGCGAAAAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCt                                      <  1:337281/137‑1 (MQ=255)                                                                                                                           ggTAACT‑TAGAGATTAGGT‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGc                          >  1:103590/1‑151 (MQ=255)                                                                                                                              aaCT‑TAGAGATTAGGC‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCCCCGGATATCGACCCATAACGCGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTcc                       >  1:601246/1‑151 (MQ=255)                                                                                                                              aaCT‑AAGAGATTAGGA‑TGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCt                         <  2:338633/149‑1 (MQ=255)                                                                                                                                actaaaagaTTGGGA‑TGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTc                        <  1:109501/143‑1 (MQ=255)                                                                                                                                    agagATTAGGA‑TGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATg                   <  2:106546/150‑1 (MQ=255)                                                                                                                                               aggggggAAAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGgcagc              <  1:158779/140‑1 (MQ=255)                                                                                                                                                      agaATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGa  >  2:475444/1‑150 (MQ=255)                                                                                                                                                       |                                                                                                                                                     ATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATG‑CGGTAACT‑TAGAGATTAGGA‑TTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGA  >  NC_000913/5013‑5307

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑