Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	5,159	0	G	A	46.7%	39.1 / 28.2	45	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (19/5);  new base A (0/21);  total (19/26)
Fisher's exact test for biased strand distribution p-value = 3.06e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATG‑AAGAAATTATGGAG‑AAAAATGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAA  >  NC_000913/5010‑5308                                                                                                                                                           |                                                                                                                                                       atcatcAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATG‑AAGAAATTATGGAG‑AAAAATGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGgaga                                                                                                                                                       <  1:103942/151‑1 (MQ=255) atcatcAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATG‑AAGAAATTATGGAG‑AAAAATGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGgaga                                                                                                                                                       <  2:27643/151‑1 (MQ=255)  ccatcaGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATG‑AAGAAATTCTGGAG‑AAAAATGACAGGAAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGgag                                                                                                                                                        >  1:201218/2‑149 (MQ=255)      caGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATG‑AAGAAATTATGGAG‑AAAAATGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATaa‑c                                                                                                                                                 <  2:445373/151‑1 (MQ=255)      caGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATG‑AAGAAATTATGGAG‑AAAAATGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATaa                                                                                                                                                   <  2:721028/150‑1 (MQ=255)      caGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATG‑AAGAAATTATGGAG‑AAAAATGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATaa                                                                                                                                                   <  2:17143/150‑1 (MQ=255)            aaTCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATG‑AAGAAATTATGGAG‑AAAAATGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAAccgc                                                                                                                                           <  2:188898/151‑1 (MQ=255)                          caaaaTCAGGCTGGTTTTGTTTTTAGCCAGCCGGTTTTTTTAATG‑AAAAAATTAGGGAA‑AAAAATGACGGGAAAAAAGGAAAAATTC‑TC‑AATAAATGCGTTAATTGAGAGATTAGGATGG‑CGGAAAAAAA‑CAACCGCCGTTCTCATCg                                                                                                                                <  1:477245/145‑1 (MQ=255)                                         tttGTTTTTATGCAGCCCGTTTTTTTTATA‑AAAAAATTAGGGAA‑AAAAAGGACAGGAAAAAAGGAAAAATTC‑TA‑AAAAAAGGCGGTAACTTAGAGATTAGGATGG‑GGGAAAAAAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGatat                                                                                                                <  2:699935/149‑1 (MQ=255)                                            gCTTTTATGCAGCCCGGCTTTTTTATG‑AAGAAATTATGGAG‑AAAAATGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAcc                                                                                                           >  1:673682/1‑151 (MQ=255)                                              ttttATGCAGCCCGGCTTTTTTATG‑AAGAAATTATGGAG‑AAAAATGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAccc                                                                                                          >  2:113916/1‑150 (MQ=255)                                                 tATGCGGCCCGGTTTTTTTATA‑AAAAAATTAGGGAA‑AAAAATGACAGGAAAAAAGGAAAAATTC‑TC‑AAAAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAAAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCAt                                                                                                        <  2:299263/149‑1 (MQ=255)                                                  acacaccccGGTTTTTTAAAA‑AAAAAATTAGGGAA‑AAAAAGGAAAGGGAAAAGGGAAAAATTC‑AA‑AAAAAAGGGGGTAATTTAGAGATGAGGTTGG‑CGGAAAAAAA‑AAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAc                                                                                                            <  1:184141/138‑1 (MQ=255)                                                         ccgttttttttAAA‑AAAAAATTATGAAA‑AAAAAAAAGAGGAAAAAAGGAGAAATTC‑AC‑AAAAAACGCGATAATTTAGAGAAGGGGATTG‑CGGAAAATAA‑CATCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGc                                                                                                 <  2:315880/143‑1 (MQ=255)                                                          ggttttttttAAA‑AAAAAATTAGGGAA‑AAAATTAAAAGGAAAAAAGAAAAATTTC‑GC‑AAAAAAGTCGTTATTTTAGAAATAGGGATGG‑GGAAAAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa                                                                                               <  1:179888/145‑1 (MQ=255)                                                            ggttttttAAGAAAAAAATTAGGGAA‑AAAAAGGACA‑GAAAAAAGGAAAAAATCAAA‑AATAATTGCGGTAAGTGAGAGATGAGGATGG‑AGGAAAAAAA‑AAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACggg                                                                                                  <  1:470467/143‑1 (MQ=255)                                                             tttttttATA‑AAAAAATTATGGAA‑AAAAAGGAGAGGAAAAAAGAAGAAATTC‑CC‑AAAAAATGGGGTAATGTAGAATTAAGGATTG‑GGAAAAAAAA‑CAGCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGAt                                                                                           <  1:5988/149‑1 (MQ=255)                                                              ttttttAAA‑AAAAAATTTAGGAAAAAAAATGCAAGGAAAAGCGGAAAAATTC‑AA‑AAAAAATGCGTTACCTAAGACATT‑GGACTGAGGGAAAAAAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATg                                                                                             <  1:256470/148‑1 (MQ=255)                                                                        aaaaaaTTAGGAAA‑AAAAAGGAGAGGAAAAAAGGAAAAATTC‑TC‑AAAAAATGCGGTAACTTAGAGATTAGGATTG‑CGAAAAAAAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAg                                                                                   <  1:498586/145‑1 (MQ=255)                                                                              ttATGGAG‑AAAAATGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgtg                                                                          >  2:716197/1‑151 (MQ=255)                                                                              ttATGGAG‑AAAAATGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgtg                                                                          >  2:224543/1‑151 (MQ=255)                                                                                taggaaaaaaaaGGAAAGGAAAAAAGGAAAAATTC‑TA‑AAAAAATGGGTTAACTTAAAGATTAGGATGG‑CGGAAAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgtg                                                                          <  1:587507/143‑1 (MQ=255)                                                                                     g‑aAAAATGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaaa                                                                      >  2:351519/1‑148 (MQ=255)                                                                                     aaaaaaatagaaGGAAAAAAGAAAAAATTC‑CA‑AAAAAATGCGTTAATTTAGAATTTAGTATTG‑CGAAAAAAAA‑CACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAg                                                                    <  1:688940/140‑1 (MQ=255)                                                                                      aaaaaaaggaaaggAAAAAGGGAAAATTC‑CCAAATAATTGGGGTAATTTAGAAATTA‑GTTTG‑GGGAAAAAAACCACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaa                                                                       <  2:391628/136‑1 (MQ=255)                                                                                       aaaaaTGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaaa                                                                      >  2:145050/1‑147 (MQ=255)                                                                                          aaTGAGAGGAAAAAAGGAAAATTTC‑CA‑AAAAAAGGCGTTAACTGAGAGATTAGGATGG‑GGGAAAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCa                                                               <  2:133453/151‑1 (MQ=255)                                                                                                aGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTAt                                                         >  1:800283/1‑151 (MQ=255)                                                                                                    aaaaaGGAAAAATTC‑TA‑AATAAAGGCGTTAATTAAGAGATTAGGATTG‑GGGAAAAAAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCg                                                       <  2:40653/149‑1 (MQ=255)                                                                                                    aaaaaGGAAAAATTC‑TA‑AAAAAAGGCGGTAACTAAGAGTTTAGGATGG‑CGGAAAAAAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCg                                                       <  2:176318/149‑1 (MQ=255)                                                                                                     aaaaGGAAAAATTC‑TC‑AAAAAAGGGGTTAACTAAGATATTAGGATTG‑CGAAGAAAAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTAc                                                    <  1:614123/151‑1 (MQ=255)                                                                                                         ggAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGc                                                >  2:522139/1‑151 (MQ=255)                                                                                                             aaaTTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACtt                                            >  1:680901/1‑151 (MQ=255)                                                                                                               aTTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTc                                          >  1:30252/1‑151 (MQ=255)                                                                                                                  c‑tc‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCt                                       >  2:17805/1‑151 (MQ=255)                                                                                                                  c‑tc‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCt                                       >  2:66811/1‑151 (MQ=255)                                                                                                                  c‑tc‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCt                                       >  1:453851/1‑151 (MQ=255)                                                                                                                       aaaaaagggggTAACTAAGAGTTTAGGATTG‑GGAAAAAAAA‑AAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCt                                       <  1:280049/139‑1 (MQ=255)                                                                                                                       aaaaaaTGCGGTAATTTAGAAATTAGAATGG‑GGGAAAAAAC‑AAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGt                                    <  2:491732/148‑1 (MQ=255)                                                                                                                       aaTAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGt                                    >  1:483822/1‑151 (MQ=255)                                                                                                                        aTAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGtt                                   >  2:416541/1‑151 (MQ=255)                                                                                                                          aaaTGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCt                                 >  2:442719/1‑151 (MQ=255)                                                                                                                           aaTGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTg                                >  2:543710/1‑151 (MQ=255)                                                                                                                              gggatAACTTAGAGATAAGGATGG‑CGAAAAAAAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTgg                               <  1:737792/145‑1 (MQ=255)                                                                                                                              gCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTc                             >  2:25508/1‑151 (MQ=255)                                                                                                                                             ttAGGATTG‑CGGAAAAAAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGgca                 <  1:161800/148‑1 (MQ=255)                                                                                                                                              tAGGATTG‑CGGAAAATAA‑CACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGgct                 <  2:571191/147‑2 (MQ=255)                                                                                                                                                     g‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGc      >  2:139243/1‑151 (MQ=255)                                                                                                                                                         gagaATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCgg    >  2:492876/1‑150 (MQ=255)                                                                                                                                                         gagaATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCgg    >  2:163935/1‑150 (MQ=255)                                                                                                                                                           gaATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGaa  >  2:133854/1‑150 (MQ=255)                                                                                                                                                           |                                                                                                                                                       ATCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATG‑AAGAAATTATGGAG‑AAAAATGACAGGGAAAAAGGAGAAATTC‑TC‑AATAAATGCGGTAACTTAGAGATTAGGATTG‑CGGAGAATAA‑CAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAA  >  NC_000913/5010‑5308

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑