Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_KO_pgi4,477,4540AT24.1% 48.5 / 10.1 29intergenic (+131/+14)rraB/yjgMprotein inhibitor of RNase E/GNAT family putative N‑acetyltransferase
Reads supporting (aligned to +/- strand):  ref base A (9/13);  new base T (2/5);  total (11/18)
Fisher's exact test for biased strand distribution p-value = 6.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CGGAGTTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGATATGCTCAAAGCCCAAATGCTCATAAAGCGCAATGGCTTCCTTTAAAAAAGCGGTCGTTTCCAGA  >  NC_000913_3_KO_pgi/4477308‑4477597
                                                                                                                                                  |                                                                                                                                               
cGGAGTTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGTGTTCAACTcg                                                                                                                                               >  1:554503/1‑149 (MQ=255)
  gAGTTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACAcgcg                                                                                                                                             <  1:397656/149‑1 (MQ=255)
    gTTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGTGTTCAACTCGCggg                                                                                                                                           <  2:554503/149‑1 (MQ=255)
         ccACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCAGCGAGTTGAACAAGCGGGCAttt                                                                                                                                      >  1:169631/1‑149 (MQ=255)
              aaTTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGTGTTCAACTCGCGGGCAttcgaaca                                                                                                                                 <  1:462875/149‑7 (MQ=39)
                ttAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTaga                                                                                                                               <  1:386182/149‑1 (MQ=255)
                      gTAGCGTATCAGGCCCAGGTTGGTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTcgc                                                                                                                         <  2:342915/149‑1 (MQ=255)
                                  gCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCa                                                                                                             <  1:353712/149‑1 (MQ=255)
                                       ggTAGTTCCTGCAACCTGGTGAATTAGCAGCCCGGATAAGGCCTTCAATACACATCCGGCATAGAAGAAACAATCTTTTTACAAAATTAAACTCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTca                                                                                                        <  1:627619/149‑1 (MQ=255)
                                          agtgcttGCAACCGGGTGAATTTGCAGCACATATAAGGCATTCATGTCCCATTCGTCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCTCGATTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACaa                                                                                                     <  2:68970/143‑1 (MQ=255)
                                              ccTGCAAACTGAAGAATTTGTAGTCTCGACTAGGCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAAAGTTCGACTGCCCCCAATTTGAAATACATATCAGTTTTTTAGAGTACGCGCAACATCCGCACTTCACAATCGa                                                                                                 <  1:628131/149‑1 (MQ=255)
                                                                  tAGCCCGGATAAGGCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAgc                                                                             >  1:231780/1‑149 (MQ=255)
                                                                     cccGGATGAGGNATTCATGTCACAGCCNGCATNAACAAAANGTACGTTGTTAATGTTCGAATGCCCGCGAGGTGAACACGCGGGCATTGTCTCAGAGTTCGCGCAACATCCGCCCTTCACAATCGACATGGCCCGTGCAGCCAAGCGCa                                                                          <  1:23242/149‑1 (MQ=255)
                                                                       cGGATAAGGCATTCCTGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATa                                                                        <  2:478566/149‑1 (MQ=255)
                                                                              ggCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGata                                                                 >  1:522774/1‑149 (MQ=255)
                                                                              ggCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGata                                                                 >  2:424547/1‑149 (MQ=255)
                                                                                 actCATCTCACATCCGGCCTAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGATATGc                                                              <  2:52583/147‑1 (MQ=255)
                                                                                 aTTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAg                                                                                   >  1:590521/1‑128 (MQ=255)
                                                                                 aTTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAg                                                                                   <  2:590521/128‑1 (MQ=255)
                                                                                             tCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCCCAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGATATGCTCAACGCCCaac                                                  >  1:460438/1‑148 (MQ=255)
                                                                                                  caaaaaCAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGTTACATTTGGGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGATATGCTCAAAGCCCAAATGCTc                                             <  1:150446/146‑1 (MQ=255)
                                                                                                       aCAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGATATGCTCAAAGCCCAAATGCTCATaaa                                        <  1:424547/149‑1 (MQ=255)
                                                                                                        cAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGATATGCTCAAAGCCCAAATGCTCATAAAg                                       >  1:411230/1‑149 (MQ=255)
                                                                                                                    tgttAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCAGTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGATATGCTCAAAGCCCAAATGCTCATAAAGCGCAATGGCTTc                           <  1:497083/149‑1 (MQ=255)
                                                                                                                         aTGTTCGGATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGATATGCTCGAAGCCCAAATGCTCATAAAGCGCAATGGCTTCCTTTa                      >  1:589654/1‑149 (MQ=255)
                                                                                                                              aaaaTGCCCGCGTGTTCAACTCGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGATATGCTCAAAGCCCAAATGCTCATAAAGCGCAATGGCTTCCTTTaa                     <  1:58927/143‑1 (MQ=255)
                                                                                                                              aaaaTGCCCGCGTGTTCAACTCGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGATATGCTCAAAGCCCAAATGCTCATAAAGCGCAATGGCTTCCTTTaa                     >  2:58927/3‑145 (MQ=255)
                                                                                                                                     ccGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGATATGCTCAAAGCCCAAATGCTCATAAAGCGCACTGGCTTCCTTTAAAAAAGCGGTCg          >  1:231419/1‑149 (MQ=255)
                                                                                                                                             ggAACTCGCGTGCAGTTTTGTAGAGGTGTCGCAACAGCCGCACTTCACAATCGCCCTGACCCGTGCCGCCAAGCGCAGAGTCGATATGCTAAAAGCCCAAGTGCTCAGAAAGCGCAATGGCTTCCTTTAAAAAAGCGGTCGTTTCCAGa  <  2:292742/148‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                               
CGGAGTTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCATAAACAAAACGTACGTTGTTAATGTTCGAATGCCCGCGAGTTGAACACGCGGGCATTTTTTTAGAGTTCGCGCAACATCCGCACTTCACAATCGACATGGCCCGTGCAGCCAAGCGCATAGTCGATATGCTCAAAGCCCAAATGCTCATAAAGCGCAATGGCTTCCTTTAAAAAAGCGGTCGTTTCCAGA  >  NC_000913_3_KO_pgi/4477308‑4477597

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑