Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,001,918	0	A	C	37.8%	57.7 / 11.6	37	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
Reads supporting (aligned to +/- strand):  ref base A (23/0);  new base C (0/14);  total (23/14)
Fisher's exact test for biased strand distribution p-value = 1.64e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAG  >  NC_000913/2001781‑2002051                                                                                                                                            |                                                                                                                                       tGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAAcc                                                                                                                                      >  1:529451/1‑140 (MQ=255)   taTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCGTGATTATCCGGTTATGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTTCAGGCAGAAAAAAAcc‑cc                                                                                                                                   >  2:956788/2‑140 (MQ=255)   aaTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAAcc‑cc                                                                                                                                   >  1:542278/1‑140 (MQ=255)    aTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑ccg                                                                                                                                  >  1:1026249/1‑140 (MQ=255)    aTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑ccg                                                                                                                                  >  1:715607/1‑140 (MQ=255)                  gCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGaa                                                                                                                    >  1:649477/1‑140 (MQ=255)                     cTGTGTTATATGAGTTATGGGCATGATTATCCTTTTCTGCGGGGTTTTTAATCGGACGATTAGGGGGGAAAAGGAGGGTTTATTGGGGGT‑TTAAAGGT‑AAATTCCAGGAAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCa                                                                                                                 <  2:649477/140‑1 (MQ=255)                      tGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCAc                                                                                                                >  1:1008106/1‑140 (MQ=255)                      tGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCAc                                                                                                                >  2:630513/1‑140 (MQ=255)                        cGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGt                                                                                                              >  2:200818/1‑140 (MQ=255)                                  gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                    >  1:1093497/1‑140 (MQ=255)                                  gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                    >  1:1007096/1‑140 (MQ=255)                                  gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                    >  1:982967/1‑140 (MQ=255)                                  gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGAACGTTGCTGACgaa                                                                                                    >  2:951828/1‑140 (MQ=255)                                   ttATCGGAATGATTATCCTTTTCTGCGGGGTTTTTAATCGGACGATTAGTGGGT‑AAAAGGGGGGTTTTTTGGGGT‑TTACAGGA‑AATTCCCAGGAAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAAtt                                                                                                  <  2:102599/140‑1 (MQ=255)                                     aTCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTT‑GGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgc                                                                                                >  1:102599/1‑140 (MQ=255)                                           aTGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCttt                                                                                           >  1:684342/1‑140 (MQ=255)                                                      tttCTGAGGGTTTTTTAAGCGGACG‑TTTGGGGGGAAAAAGGGGGGTTTTTTGGGGG‑GTAAAAGTAAAATTCCAGGAAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGa                                                                                <  2:529451/140‑1 (MQ=255)                                                        tCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATg                                                                              >  1:412726/1‑140 (MQ=255)                                                          tGCAGGTTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGTTTATTGGGGGG‑TTACAGGT‑AAATCCCAGGAAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcg                                                                            <  2:903952/140‑1 (MQ=255)                                                               ggTTTTTAATCGGACAATTGGGGGGTAAAAGGAGGGTTTTTTTGGGGG‑TTACAGGA‑AAATCCCAGGCAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTa                                                                       <  2:715607/140‑1 (MQ=255)                                                                ttttttAATGGGACGATTAGGGGGTGAAATGAGGGTTTTTTGGGGGG‑TTACAGGT‑AAATCCCAGGAAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTaa                                                                      <  2:684342/139‑1 (MQ=255)                                                                gTTTTTAATGGGACAATTAGTGGGTGAAATGGGGGTTTTTTGGGGGG‑TTACAGGT‑AAATCCGAGGAAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTaa                                                                      <  2:87298/140‑1 (MQ=255)                                                                gTTTTAAAGCGGACAATTGGGGGGAAAAATGGGGGGTTATTGGGGGG‑TTACAGCA‑AAATCCCGGGAAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTaa                                                                      <  2:685139/140‑1 (MQ=255)                                                                           gACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATcc                                                           >  1:362745/1‑140 (MQ=255)                                                                           gACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATcc                                                           >  1:207457/1‑140 (MQ=255)                                                                            aggtttggTGGGTGAAATGGGGGGTTTTTGGGGGG‑TTACAGTT‑AATTTCCAGGAAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCg                                                          <  2:1007096/133‑1 (MQ=37)                                                                            aaaaTTAGTGGGAGAAAAGGGGGGTTTTTGGGGGG‑TTACAGGT‑AAATCCCAGGCAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCg                                                          <  2:310672/137‑1 (MQ=38)                                                                                          aaaTGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACaaaaactg                                            >  1:310672/1‑137 (MQ=255)                                                                                          aaaTGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAAtgt                                            >  1:831699/1‑140 (MQ=255)                                                                                            aggggggtTTATTGGGGGG‑TTAAAGGA‑AAATCCCAGGAAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGc                                          <  2:1008106/136‑1 (MQ=37)                                                                                            aatgggggTTTTTTGGGGGTTTACAGGA‑AAATTCCAGGCAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAAtgtg                                           <  1:200818/136‑1 (MQ=37)                                                                                                    ttATTGGGGGT‑TAACAGG‑‑AAATTTCCGGAAAAAAAAACCCACCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCaa                                  <  1:956788/140‑1 (MQ=21)                                                                                                                  aCAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                     >  1:873519/1‑140 (MQ=255)                                                                                                                  aCAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                     >  1:593932/1‑140 (MQ=255)                                                                                                                   cAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                    >  2:941806/1‑140 (MQ=255)                                                                                                                              ccAGGAAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGc          <  2:982967/140‑1 (MQ=255)                                                                                                                                 ggCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTg       >  2:202788/1‑140 (MQ=255)                                                                                                                                      aaaaaaaCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAag  >  1:623347/1‑140 (MQ=255)                                                                                                                                            |                                                                                                                                       TGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGT‑AAATTCCAGGCAGAAAAAAACC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAG  >  NC_000913/2001781‑2002051

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑