Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,173,2960GC34.0% 56.9 / 41.9 47intergenic (‑289/+43)fadD‑I/fadD‑IIlong‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase
Reads supporting (aligned to +/- strand):  ref base G (19/12);  new base C (8/8);  total (27/20)
Fisher's exact test for biased strand distribution p-value = 5.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCGGTGAAGTTGG  >  NC_002947/5173160‑5173445
                                                                                                                                        |                                                                                                                                                     
cTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACACTGCCCAATGTAGGAGCg                                                                                                                                          <  2:288807/150‑1 (MQ=39)
 ttATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCgg                                                                                                                                         <  1:1069556/150‑1 (MQ=255)
   aTGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAATTTAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGt                                                                                                                                       <  1:1135392/150‑1 (MQ=255)
    tGGTCACAAAAATTACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGtt                                                                                                                                      <  1:213393/150‑1 (MQ=255)
                tGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCgaatg                                                                                                                          <  1:930543/150‑3 (MQ=37)
                    tCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGttt                                                                                                                                     >  1:1252662/1‑135 (MQ=255)
                    tCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGttt                                                                                                                                     <  2:1252662/135‑1 (MQ=255)
                             aaTACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCgg                                                                                                                                         >  1:1176555/1‑122 (MQ=255)
                             aaTACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCgg                                                                                                                                         <  2:1176555/122‑1 (MQ=255)
                                    gTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACACTGCCCAATGTAGGAGCg                                                                                                                                          <  2:554877/114‑1 (MQ=37)
                                    gTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACACTGCCCAATGTAGGAGCg                                                                                                                                          >  1:554877/1‑114 (MQ=37)
                                         ttttAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTCTATc                                                                                                 >  1:467850/1‑150 (MQ=255)
                                                 tAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACt                                                                                         >  1:1124120/1‑150 (MQ=255)
                                                       tCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCccgcc                                                                                   >  1:573877/1‑150 (MQ=255)
                                                         cAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCcgccgc                                                                                 >  1:324437/1‑150 (MQ=255)
                                                         cAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACACTGCCCAATGTAGGAGc                                                                                                                                           >  1:888890/1‑92 (MQ=25)
                                                         cAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGCTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCcgccgc                                                                                 >  1:324410/1‑150 (MQ=255)
                                                         cAAAATGTCGCAGATAAGGCTGTATAGAGCATGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACACTGCCCAATGTAGGAGc                                                                                                                                           <  2:888890/92‑1 (MQ=25)
                                                                  gCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGt                                                                                                              >  1:466235/1‑112 (MQ=255)
                                                                  gCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGt                                                                                                              <  2:466235/112‑1 (MQ=255)
                                                                  gCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGACTAATGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTg                                                                        >  1:810603/1‑150 (MQ=255)
                                                                    aGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACAATTAGCAGGGTAGGAGCGGGTTTACCCGCGAAGAAGCCATACCGGTATGACGCGATATCGCGCAACTCCCCCCCGAAACTCTTGcc                                                                      >  2:418712/1‑150 (MQ=37)
                                                                             tggataGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTggg                                                                                                                                                       >  2:901018/4‑60 (MQ=255)
                                                                             tGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTggg                                                                                                                                                       <  1:901018/60‑1 (MQ=255)
                                                                                          ttAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCCCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGAt                                                >  2:164559/1‑150 (MQ=255)
                                                                                             gagCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTcg                                             >  2:393874/1‑150 (MQ=255)
                                                                                                      aaGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCGACGATTCGCGCAGCACg                                    >  1:1312769/1‑150 (MQ=255)
                                                                                                               gcgGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCCAAGAAGTCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGTCGTCATGGGCAACGATTCGCGCAACACAATGTGCTTg                           >  2:205178/1‑150 (MQ=39)
                                                                                                                cgGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTgg                          <  2:1124120/150‑1 (MQ=255)
                                                                                                                 gggTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGa                                   <  2:15852/140‑1 (MQ=255)
                                                                                                                 gggTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGa                                   >  1:15852/1‑140 (MQ=255)
                                                                                                                       aCCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACttt                   <  2:324437/150‑1 (MQ=255)
                                                                                                                       aCCCGCTCCTACATTGGGCAGCCTATGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACttt                   <  2:324410/150‑1 (MQ=255)
                                                                                                                        cccGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCACGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTg                  >  2:33242/1‑150 (MQ=255)
                                                                                                                        cccGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAATAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTg                                                                        <  1:183517/96‑1 (MQ=21)
                                                                                                                        cccGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAATAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTg                                                                        >  2:183517/1‑96 (MQ=21)
                                                                                                                        cccGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTg                  >  2:353200/1‑150 (MQ=38)
                                                                                                                         ccGCTCCTACATTGGGCAGTGTAGGAGCGTGTTCACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCCTGGGCAACGATTCGCGCAGCACGAGGTGCTTGGGGACTTTGt                 >  2:45930/1‑150 (MQ=255)
                                                                                                                         ccGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGt                 <  1:353200/150‑1 (MQ=255)
                                                                                                                         ccGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGt                 >  2:315823/1‑150 (MQ=39)
                                                                                                                          cGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTa                <  2:573877/150‑1 (MQ=255)
                                                                                                                           gCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTcc                                                                                       <  2:1274368/78‑1 (MQ=18)
                                                                                                                           gCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTcc                                                                                       >  1:1274368/1‑78 (MQ=18)
                                                                                                                           gCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAg               >  1:1349189/1‑150 (MQ=39)
                                                                                                                           gCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAg               >  2:906380/1‑150 (MQ=39)
                                                                                                                              ccTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCGACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCg            <  2:1312769/150‑1 (MQ=255)
                                                                                                                              ccTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTgg                          <  1:764870/136‑1 (MQ=255)
                                                                                                                               cTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCgg           >  2:1244097/1‑150 (MQ=255)
                                                                                                                                  cATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCGGTGa        >  2:1171247/1‑150 (MQ=255)
                                                                                                                                        gCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCGGTGAAGTTgg  >  2:1179072/1‑150 (MQ=255)
                                                                                                                                        |                                                                                                                                                     
CTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCGGTGAAGTTGG  >  NC_002947/5173160‑5173445

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑