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%	42.3 / 70.0	46	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (18/4);  new base C (0/23);  total (18/28)
Fisher's exact test for biased strand distribution p-value = 4.26e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.62e-06

TTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATT‑CCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATT  >  NC_000913/1376358‑1376651                                                                                                                                                         |                                                                                                                                                   ttACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATT‑CCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACAccc                                                                                                                                                 >  2:447834/1‑151 (MQ=255)    ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATT‑CCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACACCCTCg                                                                                                                                              <  1:127291/151‑1 (MQ=255)            gACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATT‑CCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACACCCTCGCCGATGcc                                                                                                                                      <  1:348869/151‑1 (MQ=255)              ccTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATT‑CCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACACCCTCGCCGATGccc                                                                                                                                     >  2:168248/1‑150 (MQ=255)               cTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATT‑CCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACACCCTCGCCGATGCccgc                                                                                                                                   >  2:802656/1‑151 (MQ=255)                 cgccgcGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATT‑CCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACACCCTCGCCGATGCccgcc                                                                                                                                  <  1:41251/150‑1 (MQ=255)                   ccgcGTCGCCGGGCGGGCGACGGAAAAAGGTTGGGTGATC‑CCCTGCGCGTCCTGGAACAGGTCGCCGCGCGTCCCGGAA‑CCGTGGTGTACCTCAAACCGTTAAA‑CCGC‑T‑ATCAGGATGATATGATCAACCCCCTCACCGAGGCCCGCCGt                                                                                                                                <  2:247387/150‑1 (MQ=255)                       gTAGCCTGGACGGCGCCCGCAAAAGGGTGAGTGATT‑CCCTGCGCGTACTGGAACAGGTCCCCGCGCGCACCGGAC‑CCGTGGTGTATCTCGACCGTTTAAC‑CCGC‑T‑ACCAGGTTCATATGATCAACACCCTCGCCGATGCccgccg                                                                                                                                 <  2:104673/145‑1 (MQ=255)                        tAGCCTGGACGGCGACCGCAAAATGGTGAGTGATT‑CCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACAtc                                                                                                                          >  2:483655/1‑151 (MQ=255)                              ggACGGCGACCGCAAAATGGTGAGTGATT‑CCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGa                                                                                                                     >  1:596155/1‑150 (MQ=255)                                  ggCGACCGAAAATGGGTGAGTGATC‑CCCTGCGCGTACTGAAAAAGGTCGCCGCGCGTACCGGAC‑CCGTGGTGTATCCCGAACCTTAAAA‑CCGC‑T‑ATCAGGATCATATGATAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAAc                                                                                                                 <  1:262309/150‑1 (MQ=255)                                  ggCGACCGAAAAATGGTGATTTTTT‑CCCTGCGCGTACTGAAACGGGCCGCCGCGCGTCCCGGAC‑CGGTGGTGTATCCCAACCCTTTAAA‑CCGC‑T‑ATCAGGATAATATGATCACCCCCCCCGCCGTTGCCCGCCGTTACATCGTCGAAAAc                                                                                                                 <  1:344748/150‑1 (MQ=255)                                           aaaggggTGTGTGTTC‑CCCTGCGCTTCGGGAAACGGGCCCCCGCGCGACCCGGAC‑CGGGGGTGTTCCTCG‑ACCCATAAA‑CCCC‑TAACCAGTATAATATGAAAACCCCCCTCGCCGACGCCCGCCGTTACATCGTCGAAAACGATCt                                                                                                            <  2:333375/141‑1 (MQ=255)                                           aaaaTGGTGAGTGATT‑CCCTGCGCGTACTGGAACAGGGCGCCGCGCGTACCGGAA‑CCGAGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGACCATATGATCAACACCCTCGACGATGCCCGCCGTTACATCGGCGAAAACGATCTTaaa                                                                                                        >  2:765240/1‑150 (MQ=255)                                           aaaaGGGTGAG‑GATTCCCCGGCGCGTACTGGAACGGGTCGCCGGGCGTCCCGGAA‑CGGTGGTGTATCTCGACCCGTTAAC‑CCGC‑T‑ATCAGGATAATATGACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAAc                                                                                                       <  1:957412/151‑1 (MQ=255)                                            aaaTGGTGGGTGATC‑CCCGGCGCGTACGGGAACGGGCCCCCGCGCGTACCGAAA‑CGGTGGTGTACCTCGACCCTTTAAA‑CCGC‑T‑ATCAGGATCATATGAAAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACa                                                                                                      <  1:974987/151‑1 (MQ=255)                                                ggTGAGTGATT‑CCCTGCGCGTCCTGGAACAGGTCGCCGCGCGTACGGGAC‑CCGTGGTGTATCTCGACCCGTAAAC‑CCGC‑T‑ATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATg                                                                                                    <  1:427774/149‑1 (MQ=255)                                                         tt‑CCCTGCGCGTACTGGAACAGGCCGCCGCGCGTCCCGGAC‑CGGTGGTGTATCTCGACCCGTTAAA‑CCGC‑T‑ATCAGGATCATATAACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTAt                                                                                          <  1:615912/150‑1 (MQ=255)                                                                           aaCAGGCCGCGGCGCGTACCGGAA‑CGGGGGTGTTCCTCGACCCTTTAAC‑CCGT‑T‑ATAAGAATCATATAACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTa                                                                              <  2:157834/145‑1 (MQ=255)                                                                               gtctgccccGCGTACCGAAC‑CCGTGGTTTA‑ATCCTACCTTTAAA‑CCCCTT‑GTAAGCCTCATATTTCAAACTCCATCCCCGAGCCCCGCCGTTACATCGTCTAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGaa                                                                     <  1:600744/146‑1 (MQ=255)                                                                               ggTCCCCGCGCGT‑CCGGAACCCGTGTTTTATCTCGAACCTTTAAC‑CCGC‑T‑ATCAGTATCATATGATAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGa                                                                      <  1:289839/149‑1 (MQ=255)                                                                                  cgccgcGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATc                                                                 >  2:710117/1‑151 (MQ=255)                                                                                   gccgcGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCg                                                                >  1:550015/1‑151 (MQ=255)                                                                                    ccgcgctaccaggAA‑CGGGGTTGTATCTCAAACTTTAAAC‑CCTT‑T‑ATCAGAATAATATTATAACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATc                                                                 <  2:566515/138‑1 (MQ=255)                                                                                    ccgcGCTTCCCGGAC‑CGGTGGTGAATCCCGACCCTTAAAC‑CCGC‑T‑ACCGGAATCTTTGGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAatat                                                                  <  1:906959/148‑1 (MQ=255)                                                                                    ccgcGCTTACCGGAC‑CCGTGGTTTATCTCGACCCGTAAAC‑CCGC‑T‑ATCAGATTCATATGACAACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCg                                                                <  1:467082/150‑1 (MQ=255)                                                                                          gTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                            >  1:123212/1‑148 (MQ=255)                                                                                             ccGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGCTCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATa                                                       >  2:330011/1‑150 (MQ=255)                                                                                               ggAA‑CCGTGGTGTATCTCGAACCTTTAAC‑CCGC‑T‑ATCAGGATCATATGAACAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATa                                                       <  1:48128/148‑1 (MQ=255)                                                                                                 aa‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                                  >  1:195329/1‑151 (MQ=255)                                                                                                  acccGTGGTGTATCTC‑AACCCTTAAACCCGA‑T‑ATCAGGATCATATGACAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                                  <  1:341068/149‑1 (MQ=255)                                                                                                  acccGTGGTGTATCCCGACCCTTAAAC‑CCGC‑T‑ATAAGAATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCt                                                   <  1:802677/148‑1 (MQ=255)                                                                                                               ctcGACCCTTAAAC‑CCGC‑T‑ATAAGGATCATATGACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGgcgc                                        <  1:640682/148‑1 (MQ=255)                                                                                                                 caaccctttAAC‑CCCC‑T‑ATAAGGATCATATGATCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCa                                    <  2:250013/143‑1 (MQ=255)                                                                                                                            acccGC‑T‑ATCAGGATCATATGACCAACCCCCGCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgcg                         <  2:52570/149‑1 (MQ=255)                                                                                                                               cGC‑T‑ATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGAcc                      >  1:223888/1‑151 (MQ=255)                                                                                                                                      tCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTc                 >  2:748353/1‑151 (MQ=255)                                                                                                                                       cAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCg                >  2:423421/1‑151 (MQ=255)                                                                                                                                        aGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCgg               >  2:604562/1‑151 (MQ=255)                                                                                                                                        aGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCgg               >  2:239412/1‑151 (MQ=255)                                                                                                                                         ggATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGt              >  2:536005/1‑151 (MQ=255)                                                                                                                                         ggATAATATAATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCg                <  1:110663/149‑1 (MQ=255)                                                                                                                                              atatGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCa            <  1:53773/148‑1 (MQ=255)                                                                                                                                                atGACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCgg               <  2:123209/143‑1 (MQ=255)                                                                                                                                                     cAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATAtt  >  2:76049/1‑151 (MQ=255)                                                                                                                                                      aaCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCata    <  1:56157/148‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                                   TTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATT‑CCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGC‑T‑ATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATT  >  NC_000913/1376358‑1376651

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑