Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AE0154514,974,4380A.48.3% 54.1 / 54.3 29coding (1166/2043 nt)flgKFlagellar hook‑associated protein FlgK
Reads supporting (aligned to +/- strand):  ref base A (8/7);  new base . (6/8);  total (14/15)
Fisher's exact test for biased strand distribution p-value = 7.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.46e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CCAGCGTAGGTTGGGTGATGGTGCCGGTACCGCTGTTGCCACTGCCTGCCGCAGCACTGATCGGCCCGGCGAAGGCCAGTTTGTTGGCATCGGTCAGGGTGGTGGTGATGCTGCCGGCTGCCGCACGGGTAGGGATCACCTTGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGATTGCCGGAGCCTGCACTGTTGTTCGACGAGGCCAGGCTGCGCTGGGCAATGGCGGTGGCGCTGTTGATGCTGGAGAACAGCGAGCTGCCGAACTGGCCGT  >  AE015451/4974217‑4974660
                                                                                                                                                                                                                             |                                                                                                                                                                                                                              
ccAGCGTAGGTTGGGTGATGGTGCCGGTACCGCTGTTGCCACTGCCTGCCGCAGCACTGATCGGCCCGGCGAAGGCCAGTTTGTTGGCATCGGTCAGGGTGGTGGTGATGCTGCCGGCTGCCGCACGGGTAGGGATCACCTTGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTACCGGGTCGGCATTCAg                                                                                                                                                                                                                               >  1:304350/1‑223 (MQ=255)
                                                        cTGATCGGCCCGGCGAAGGCCAGTTTGTTGGCATCGGTCAGGGTGGTGGTGATGCTGCCGGCTGCCGCACGGGTAGGGATCACCTTGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCAcc                                                                                                                                                         <  1:362118/237‑1 (MQ=255)
                                                              ggCCCGGCGAAGGCCAGTTTGTTGGCATCGGTCAGGGTGGTGGTGATGCTGCCGGCTGCCGCACGGGTAGGGATCACCTTGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCCCACTGTACTGGCTTGCGCTGGTGAAc                                                                                                                                                               >  2:400849/1‑225 (MQ=255)
                                                                                   ttgGCATCGGTCAGGGTGGTGGTGATGCTGCCGGCTGCCGCACGGGTAGGGATCACCTTGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAgcggc                                                                                                                                                                                            <  1:112123/175‑1 (MQ=255)
                                                                                                            tgctgcCGGCTGCCGCACGGGTAGGGATCACCTTGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTC‑‑GTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGAtt                                                                                                    <  1:404348/236‑1 (MQ=255)
                                                                                                              ctgccggctgccgCACGGGTAGGGATCACCTTGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTC‑‑GTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCtcgtagtcg                                                                                                                                                >  1:422607/1‑190 (MQ=255)
                                                                                                              ctgccggctgccgCACGGGTAGGGATCACCTTGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTC‑‑GTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCtcgtagtcg                                                                                                                                                <  2:422605/190‑1 (MQ=255)
                                                                                                                gccggctgccgCACGGGTAGGGATCACCTTGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTC‑‑GTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGATTGCCgg                                                                                               >  1:277377/1‑237 (MQ=255)
                                                                                                                          gaaCGGGTAGGGATCACCTTGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGACTGAAGCCGTCTATCACCGGTGCCGGGTCGGCATTC‑‑GTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGgcgc                                                                                                                                                                                          <  1:294981/134‑1 (MQ=255)
                                                                                                                                   gggATCACCTTGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGATTGCCGGAGCCTGCACTgttgtt                                                                               >  1:254808/1‑236 (MQ=255)
                                                                                                                                            ttGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGCCGGCATTC‑‑GCCGAAGCTGCCCATGTCGGTGCCGTCTGGgcggcggtc                                                                                                                                                                                        >  2:48446/1‑117 (MQ=255)
                                                                                                                                            tagAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCtcgtagtcgtag                                                                                                                                             >  2:59983/3‑165 (MQ=255)
                                                                                                                                             tGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGGCGGAgggggt                                                                                                                                        >  2:110901/1‑169 (MQ=255)
                                                                                                                                             tGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTC‑‑GTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAg                                                                                                       >  1:50390/1‑200 (MQ=255)
                                                                                                                                              gAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGAtt                                                                                                    >  1:377811/1‑204 (MQ=255)
                                                                                                                                              gAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGAtt                                                                                                    <  2:377809/204‑1 (MQ=255)
                                                                                                                                                aGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCTGTGCCGGGTCGGCCTTCAGGTCGAAGCt                                                                                                                                                                                                                      <  2:110909/88‑1 (MQ=255)
                                                                                                                                                aGCTGTCGCCGGCCCCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTC‑‑GTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGAtt                                                                                                    <  1:126684/200‑1 (MQ=255)
                                                                                                                                                   tggcGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTC‑‑GTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACGCTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATcc                                                                                                         <  1:48446/189‑1 (MQ=255)
                                                                                                                                                   tGNCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGAtt                                                                                                    <  1:77962/199‑1 (MQ=255)
                                                                                                                                                      cGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTC‑‑GTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGATTGCCGGAGCCt                                                                                          <  1:357709/204‑1 (MQ=255)
                                                                                                                                                                                                   cTAGCACCGGTGCCGGGTCGGCATTC‑‑GTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGATTGCCGGAGCCTGCACTGTTGTTCGACGAGGcc                                                                     <  2:50390/180‑1 (MQ=255)
                                                                                                                                                                                                     aTCACCGGTGCCGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGATTGCCGGAGCCTGCACTGTTGTTCGACGAGGCCAGGCTGCGCTGGGCAATGGCGGTGGCGCTGTTGCTGCTGGAGAACAGCGAGCTGcc             >  2:214784/1‑236 (MQ=255)
                                                                                                                                                                                                         ccGGTGCCGGGTCGGCATTC‑‑GTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCtcgtagtcg                                                                                                                                                <  2:362343/99‑1 (MQ=255)
                                                                                                                                                                                                         ccGGTGCCGGGTCGGCATTC‑‑GTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCtcgtagtcg                                                                                                                                                >  1:362345/1‑99 (MQ=255)
                                                                                                                                                                                                               ccGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCCGCGCACCGCTGTTGGCGATGGTGACATCCAGATTGCCGGAg                                                                                             >  2:69758/1‑146 (MQ=255)
                                                                                                                                                                                                               ccGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGATTGCCGGAGCCTGCACTGTTGTTCGACGAGGCCAGGCTGCGCTGGGCAATGGCGGTGGCGCTGTTGATGCTGGAGAACAGCGAGCTGCCGAACTGGCCGt  <  1:426798/237‑1 (MQ=255)
                                                                                                                                                                                                               ccGGGTCGGCATTC‑‑GTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGATTGCCGGAGCCTGCACTGTTGTTCGACGAGGCCAGGCTGCGCTGGGCAATGGCGGTGGCGCTGt                                      >  1:85772/1‑199 (MQ=255)
                                                                                                                                                                                                                   gTCNGCANTCANGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGATTGCCGGAGCCTGCACTGTTGTTCGACGAGGCCAGGCTGCGCTGGGCAATGGCgg                                               <  1:7409/188‑1 (MQ=255)
                                                                                                                                                                                                                             |                                                                                                                                                                                                                              
CCAGCGTAGGTTGGGTGATGGTGCCGGTACCGCTGTTGCCACTGCCTGCCGCAGCACTGATCGGCCCGGCGAAGGCCAGTTTGTTGGCATCGGTCAGGGTGGTGGTGATGCTGCCGGCTGCCGCACGGGTAGGGATCACCTTGAAGCTGTCGCCGGCCGCCAGGCCGCCGCCTTTCAACGCCAGGCTGAAACCGTCTATCACCGGTGCCGGGTCGGCATTCAGGTCGAAGCTGCCCATGTCGGTGCCGTCTGAGCGGCGCACACTGTACTGGCTGGCGCTGGTGAACTTCACCTCGTAGTCGTAGGTGGTCAGCGCACCGCTGTTGGCGATGGTGACATCCAGATTGCCGGAGCCTGCACTGTTGTTCGACGAGGCCAGGCTGCGCTGGGCAATGGCGGTGGCGCTGTTGATGCTGGAGAACAGCGAGCTGCCGAACTGGCCGT  >  AE015451/4974217‑4974660

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑