Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,228,2040TA41.9% 44.1 / 10.5 31I135N (ATC→AAC) ygjJputative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base T (0/18);  new base A (12/1);  total (12/19)
Fisher's exact test for biased strand distribution p-value = 9.21e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑AATGGT‑GGGGCGATTTCACCCCCGATCTGGGCTACGT‑CA‑TTCCCAATACCCGCGACATTATGACTGCGCTGAAGGTACAGAACTTAAGCGGCAACTTTCG  >  NC_000913/3228057‑3228345
                                                                                                                                                   |                                                                                                                                                 
ccTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCAt                                                                                                                                                <  2:277530/151‑1 (MQ=255)
       cGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCTGTTATCGTACCAATGATGGCACCGAAATCATGCTCAg                                                                                                                                          <  2:145760/150‑1 (MQ=255)
       cGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAg                                                                                                                                          <  1:529882/150‑1 (MQ=255)
         gCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGATTTCGTACCAATGATTGGGCCCAAAACATCCTc                                                                                                                                            >  1:363225/1‑146 (MQ=255)
                 tACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAg                                                                                                                                <  2:151606/150‑1 (MQ=255)
                        aaGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTTTCGTACCCACGAAGGGACCCAAAACAAGCCCAGCCTGCCTCAGGGtttccc                                                                                                                        >  2:221959/1‑147 (MQ=255)
                        aaGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTc                                                                                                                        <  2:301228/151‑1 (MQ=255)
                                      cAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATAGTACCCAAGATGGGGCCGCAAACATTCCCCCTCTTCGTCAGGGGTCCCCGCTGGGTGGCCCGc                                                                                                          >  2:227250/1‑151 (MQ=255)
                                        ggCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑aa                                                                                                       <  2:86449/151‑1 (MQ=255)
                                          ccGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑AAtg                                                                                                     <  1:594466/151‑1 (MQ=255)
                                          ccGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑AAtg                                                                                                     <  2:690102/151‑1 (MQ=255)
                                                 cgacgGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑AATGGT‑GGGGc                                                                                             <  2:173345/151‑1 (MQ=255)
                                                         aTGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATTGTACTCATGAGGGGACAGGAAATATTAACACTTTGCGTCTGGATTTCTTGCTGGGTGAGCTGC‑GAAGGA‑gggggg                                                                                            >  2:269507/1‑142 (MQ=255)
                                                                ggTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGGTTTTGTAACCAAGATGGGGCCGCAAACATGCTCCGTCTGCGTCTGGATTTCTCGCCCGGTGAACTGC‑CATGGT‑GGGGGGGGTTTAccccc                                                                                 >  2:137855/1‑148 (MQ=255)
                                                                 gTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑AATGGT‑GGGGCGATTTCACCCCCGATc                                                                             <  1:44450/151‑1 (MQ=255)
                                                                  tGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATTCTACCAATAATGGGACCCAAAACAATCTCCAGCTGCGTCAGGGATTCTCCCCGGGTGAACCGCAAATGGG‑GGGGGGTTTTTAcccccatc                                                                              >  2:537571/1‑147 (MQ=255)
                                                                   gCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑AATGGT‑GGGGCGATTTCACCCCCGATCt                                                                            <  2:558184/150‑1 (MQ=255)
                                                                    ccAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑AATGGT‑GGGGCGATTTCACCCCCGATCTgg                                                                          <  1:172856/151‑1 (MQ=255)
                                                                     cAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑AATGGT‑GGGGCGATTTCACCCCCGATCTggg                                                                         <  1:614968/151‑1 (MQ=255)
                                                                     cAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑AATGGT‑GGGGCGATTTCACCCCCGATCTggg                                                                         <  1:369345/151‑1 (MQ=255)
                                                                     cAGACCAGAGCTTGGGTGGTATCGACGGCGGCAGTAACCATTTCTATTGCGGTTATCGTACCAATGATGGCACCGAAAACATTCTCAGACAGCGTCAGGATTCCGCGCTGGATTAAATGC‑AATGGT‑GGTGAGATTTCAccccc                                                                                 <  1:601596/143‑1 (MQ=255)
                                                                        aCCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATTGTACCAAAAATGGGCCCGAAAACATTCTCCGTCTGCGTCAGGATTTCTCCCCGGGTGAACTGC‑CAAGGT‑GGGGGGGTTTTAccccccctc                                                                             >  2:110065/1‑140 (MQ=255)
                                                                            tAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATTGTACCAAATATGGGACCCAAAACAATCTCAATCTGCGTCAGGGTTTCTCCCCGGGTGACCTGC‑AAAGGT‑GGGGGGGTTTTTccccccctcttgggcac                                                                     >  2:37047/1‑136 (MQ=255)
                                                                                 ggggTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑AATGGT‑GGGGCGATTTCACCCCCGATCTGGGCTACGT‑CA‑TTcc                                                           <  2:675818/151‑1 (MQ=255)
                                                                                      ggtTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑AATGGT‑GGGGCGATTTCACCCCCGATCTGGGCTACGT‑CA‑TTCCCAATa                                                      <  1:479802/151‑1 (MQ=255)
                                                                                           cGAGGGCGGAATTAACCGTTTCTATGGCGGTTTTTCTACCAATGATGGGGCCGGAAAAATGATCACTTTTCGTTCGGGTTTCTCGCCGGGGGGCCCGC‑CATGGTGGGGGGGGTTTCCCCCCCCTCCTGGGC‑ACGTCCT‑TTCCCAAAAcccc                                                  >  1:574101/1‑150 (MQ=255)
                                                                                           cGAGGGCGGAATTAACCGTTTCTATGGCGGTTTTCGTAACCAAGAAGGGACCGAAAACATGCTCAGGCTGCGTCAGGGGTCCTCCCTGGATGAGCTGC‑AAAGGG‑GGGGGGGGTTCACCCCCCCTCTGGGGTACGTCCT‑TTCCCAAAAcccc                                                  >  2:301638/1‑150 (MQ=255)
                                                                                            gAGGGCGGAATTAACCGTTTCTATGGCGGTTTTTGTACCAAAGAAGGGACCGAAAACAAGCTCCATTTGCGTCACGGTTTCTCGCCGGGTGACCTGC‑AAAGGG‑GGGGGGGGTTCCCCCCCCCTCTTGGGTACGC‑CATTTCCCAAAAcccc                                                  >  2:491832/1‑149 (MQ=255)
                                                                                                    aaTTAACCGTTTCTATGGCGGTTATTGTACCAAAGATGGCAACGCAAACAAGCTCAGTCTGCGTCAGGAGTTCTCGCCGGAGGAACCGC‑CATGGG‑GGGGGGGTTTTAACCCCCACCTTGGGTAAGT‑CA‑TTCCCAAAACCcccggc                                              >  2:705328/1‑143 (MQ=255)
                                                                                                       tAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑AATGGT‑GGGGCGATTTCACCCCCGATCTGGGCTACGT‑CA‑TTCCCAATACCCGCGACATTATGAc                                      <  1:58360/150‑1 (MQ=255)
                                                                                                                                          gCACCGAAATCATGCTCAGTCAGCGTCAGGATTCCTCGCTGGATGACCTGC‑AATGGT‑GGGGCGATTTCACCCCCGATCTGGGCTACGT‑CA‑TTCCCAATACCCGCGACATTATGACTGCGCTGAAGGTACAGCACTTAAGCGGCAACTTTCg  <  1:142003/151‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                 
CCTGGTTCGGCCTGATTTACGGCGAAGGCTGGACCGTGCAGGCCGACCACGACGGCAATGCCTGGGTGCCAGACCATAGCTGGGGTGGTTTCGAGGGCGGAATTAACCGTTTCTATGGCGGTTATCGTACCAATGATGGCACCGAAATCATGCTCAGTCTGCGTCAGGATTCCTCGCTGGATGACCTGC‑AATGGT‑GGGGCGATTTCACCCCCGATCTGGGCTACGT‑CA‑TTCCCAATACCCGCGACATTATGACTGCGCTGAAGGTACAGAACTTAAGCGGCAACTTTCG  >  NC_000913/3228057‑3228345

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑