Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	51.1%	47.8 / 76.5	45	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (19/3);  new base C (0/23);  total (19/26)
Fisher's exact test for biased strand distribution p-value = 6.32e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.90e-07

CTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATG  >  NC_000913/1376357‑1376643                                                                                                                                                       |                                                                                                                                           cTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACAcc                                                                                                                                          >  1:749002/1‑151 (MQ=255)   tACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACAccc                                                                                                                                         >  2:33591/1‑150 (MQ=255)       gccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGGACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGcc                                                                                                                                    >  1:220195/1‑151 (MQ=255)          gATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGAt                                                                                                                                 <  1:188873/151‑1 (MQ=255)          gATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGAt                                                                                                                                 <  1:520049/151‑1 (MQ=255)             gACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGcc                                                                                                                              >  1:938506/1‑151 (MQ=255)                         tAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACAtc                                                                                                                  >  1:727978/1‑151 (MQ=255)                            ccgggcgggCGCCCGAAAATGGGTGAGTGATCCCCTGCGCGTACGGAAACGGTTCGCCGCGCGTCCCGGACCCGTGGTGTATCCCGACCCTTAAAC‑CCGC‑TATCGGGTTAATATAATAAACCCCCCCGCCGATGCCCGCCGTTACAtc                                                                                                                  <  2:709718/141‑1 (MQ=255)                              gggcgggccaccaaaaaaGGGTGAGTGTTCCCCTGCGCGTACGGGAACGGGGCGCCGCGCGTCCCGGACCCGTGGTGTATCGCGACCCTTAAAC‑CCGT‑TATCAGGAAAATAGGAACAACCCCCCCGCGGATGCCCGCCGTTACAtcgt                                                                                                                <  2:205607/134‑1 (MQ=255)                                   ggCGACCGAAAAGTGTGGAGTGTTCCCCGGCGCGTACTGAAACGGGGCCCCGCGCGTCCCGGACCCGTGGTGTATCTCGAACTTTTAAC‑CCGC‑TATCAGAATAATATAACCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAAc                                                                                                         <  2:967003/150‑1 (MQ=255)                                   ggCCACCGAAAAAGGGTGAGTGTTCCCCTGCTCGTCCTGAAACGGGCGCCCGCGTGTCCCGGACCGGGGTTTTCTCTCG‑ACCGTTAAACCCGT‑TACCAGGATAAAAGGATAAACCCCCTCCCGGATGCCCGCCGTTACATCGTCGaaa                                                                                                           <  2:775590/148‑1 (MQ=255)                                        ccGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                   >  2:943280/1‑151 (MQ=255)                                              aaTGGTGAGTGATTCCCTGCGCGTACGGAAACAGGTCGCCGCGCGTCCCGGACCCGTGGTGTATCTCGAACCTTTAAC‑CCGC‑TATCAGGATCATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACAt                                                                                             <  1:922914/151‑1 (MQ=255)                                                 ggggggtgtTTCCCTGCGCGTACGGAAACAGGCCGCCGCGCGTACCGAAACTGTGGTGTATCTCG‑ACCGTTAAACCCGC‑TATCGGGACCATATAAACAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGt                                                                                           <  2:397285/145‑1 (MQ=255)                                                 ggggagtgaTCCCCGGCGCGTACTGGAACGGGTGGCCGCGCGTACCGGAACCGTGGTGTATCCCGACCCTTTAAC‑CCGC‑TATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATg                                                                                            <  1:421069/146‑1 (MQ=255)                                                       tgtttCCCTGCGCGTACGGGAACAGGTCGCCGCGCGTCCCGGACCGGTGGTGTATCTCGACCCGTAAAC‑CCGT‑TATCGGGATCATATGATCACCCCCCACGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACa                                                                                        <  2:570163/144‑1 (MQ=255)                                                       tgaTTCCCTGCGCGTACTGGAACGGGTCGCCGCGCTTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATAAGGTTCATAAAATAAACCCCCTCGCCTAGCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACa                                                                                        <  1:719308/147‑1 (MQ=255)                                                        gaTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                    >  1:947610/1‑150 (MQ=255)                                                         aTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTAt                                                                                  >  2:360487/1‑151 (MQ=255)                                                          ttCCCGGCGCGTACTGGAACAGGTCGCCGCGCGTCCCGGACCGGTGGTTTATCTCGACCCTTTAAC‑CCGC‑TATAAGGATCATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                    <  1:921604/148‑1 (MQ=255)                                                          tccccTGCGCGTACGGAAACGGGCCGCCGCGCGTCCCGGAACGGTGGTTTATCCCAACCCGTAAAC‑CCGC‑TATCGGAATCATATAATCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACAt                                                                                             <  1:960309/137‑1 (MQ=255)                                                            cccGGCGCGTACGGAAACGGGTCGCGGCGCGTCCCGAACCGGTGGTGTATCTCAAACCTTAAAC‑CCGC‑TATCAGGATAATATAACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATc                                                                                 <  1:596764/149‑1 (MQ=255)                                                             ccTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGc                                                                              >  1:671281/1‑151 (MQ=255)                                                                gcgctttggggAACGGGCGGCCGCGCGTACGGAACCCGTGGTTTCTCCCGACCCGTAAAA‑CCGT‑TATGAGGATAAAAAGATCAACACCCGTGCGGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTAt                                                                                  <  2:122485/135‑1 (MQ=255)                                                                 cgcgTACTGAAACAGGTCCCCGCGCGTACCGGACCCGTGGTGTATCTCGAACCTTAAAC‑CCGC‑TATAAGGATAATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAtt                                                                          <  1:822939/151‑1 (MQ=255)                                                                  gcgTACTGGAACAGGCCGCCGCGCGTCCCGGACCCGTGGTGTATCTCAACCCGTTAAC‑CCGC‑TACCAGGATAATATGACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAtt                                                                          <  1:731623/150‑1 (MQ=255)                                                                       gtaaaacggggcccggcgcgTACCGGAACGGTGTTTTATCCCAACCCTTTAAC‑CCGC‑TATAGGGATAATATAACAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTAt                                                                     <  2:991626/135‑1 (MQ=255)                                                                                gttgccgcGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAat                                                            >  2:500864/4‑150 (MQ=255)                                                                                     cgcgggTACCGGAACCGGGGTGTTTCCCGAACCGTTAAA‑CCGC‑TAACAGGATAAAAAGATCAACCCCCCCCCCGGTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAatat                                                          <  2:586204/147‑1 (MQ=255)                                                                                     cgcgcgTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCga                                                       >  2:320831/1‑150 (MQ=255)                                                                                          gtgccgaaggcGTGTTTTACCTCAAACCTTAAAC‑CCGT‑TATGAGGATAATATAATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAGACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaa                                                      <  2:82220/136‑1 (MQ=255)                                                                                          gTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                    >  2:81380/1‑148 (MQ=255)                                                                                            aCCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGAt                                                >  1:315031/1‑150 (MQ=255)                                                                                             cgggAACCGTGGTTTATCCCG‑ACCTTTAAACCCGT‑TATAGGAATCAAATATCCACCCCCCCCGCCAATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGaagaag                                                  <  2:364787/145‑1 (MQ=255)                                                                                                   ctgtggttTTTCTCGAACCTTTAAC‑CCGC‑TATCAGGATCATATGAACAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                         <  1:925770/148‑1 (MQ=255)                                                                                                   cggtggtgTATCTC‑AACCCTTAAA‑CCCCTTACAAGAATAATATGAACAACCCCCCCCCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                         <  1:491192/148‑1 (MQ=255)                                                                                                                        taaacccGC‑TATCAGGATAATATGACCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACaa                      <  1:478694/144‑1 (MQ=255)                                                                                                                         ttaagccgttcatgggATAATATGATCAACCCCCGCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCa                            <  2:322466/129‑1 (MQ=255)                                                                                                                              cGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGAcc              >  1:459395/1‑151 (MQ=255)                                                                                                                              cGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGAcc              >  1:410019/1‑151 (MQ=255)                                                                                                                                       ggATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCGGGCGCAGGCGCTGCATGACAACCGCGACCTGCTc         >  2:648941/1‑148 (MQ=255)                                                                                                                                       ggATAATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTc         <  1:17526/148‑1 (MQ=255)                                                                                                                                        gATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTc     >  2:820592/1‑151 (MQ=255)                                                                                                                                           cATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtg  >  1:477836/1‑151 (MQ=255)                                                                                                                                           cATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtg  >  2:281429/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                           CTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑TATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATG  >  NC_000913/1376357‑1376643

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑